I almost have it working. It pairs programmatically but I can't get rid of the "Pairing request" notification. Some answers to this question claim to be able to hide it just after it is shown using the hidden method cancelPairingUserInput() but that doesn't seem to work for me.

Edit: Success!

I eventually resorted to reading the source code of BluetoothPairingRequest and the code that sends the pairing request broadcast and realised I should be intercepting the ACTION_PAIRING_REQUEST. Fortunately it is an ordered intent broadcast so you can intercept it before the system does.

Here's the procedure.

1. Register to receive BluetoothDevice.ACTION_PAIRING_REQUEST changed broadcast intents. Use a high priority!
2. Connect to the device.
3. Discover services.
4. If you have disconnected by now, it's probably because the bond information is incorrect (e.g. the peripheral purged it). In that case, delete the bond information using a hidden method (seriously Google), and reconnect.
5. Try to read a characteristic that requires encryption MitM protection.
6. In the ACTION_PAIRING_REQUEST broadcast receiver, check that the pairing type is BluetoothDevice.PAIRING_VARIANT_PIN and if so, call setPin() and abortBroadcast(). Otherwise you can just let the system handle it, or show an error or whatever.

Here is the code.

/* This implements the BLE connection logic. Things to watch out for:1. If the bond information is wrong (e.g. it has been deleted on the peripheral) then   discoverServices() will cause a disconnect. You need to delete the bonding information and reconnect.2. If the user ignores the PIN request, you get the undocumented GATT_AUTH_FAILED code. */public class ConnectActivityLogic extends Fragment{    // The connection to the device, if we are connected.    private BluetoothGatt mGatt;    // This is used to allow GUI fragments to subscribe to state change notifications.    public static class StateObservable extends Observable    {        private void notifyChanged() {            setChanged();            notifyObservers();        }    };    // When the logic state changes, State.notifyObservers(this) is called.    public final StateObservable State = new StateObservable();    public ConnectActivityLogic()    {    }    @Override    public void onCreate(Bundle savedInstanceState)    {        super.onCreate(savedInstanceState);        // Tell the framework to try to keep this fragment around        // during a configuration change.        setRetainInstance(true);        // Actually set it in response to ACTION_PAIRING_REQUEST.        final IntentFilter pairingRequestFilter = new IntentFilter(BluetoothDevice.ACTION_PAIRING_REQUEST);        pairingRequestFilter.setPriority(IntentFilter.SYSTEM_HIGH_PRIORITY - 1);        getActivity().getApplicationContext().registerReceiver(mPairingRequestRecevier, pairingRequestFilter);        // Update the UI.        State.notifyChanged();        // Note that we don't actually need to request permission - all apps get BLUETOOTH and BLUETOOTH_ADMIN permissions.        // LOCATION_COARSE is only used for scanning which I don't need (MAC is hard-coded).        // Connect to the device.        connectGatt();    }    @Override    public void onDestroy()    {        super.onDestroy();        // Disconnect from the device if we're still connected.        disconnectGatt();        // Unregister the broadcast receiver.        getActivity().getApplicationContext().unregisterReceiver(mPairingRequestRecevier);    }    // The state used by the UI to show connection progress.    public ConnectionState getConnectionState()    {        return mState;    }    // Internal state machine.    public enum ConnectionState    {        IDLE,        CONNECT_GATT,        DISCOVER_SERVICES,        READ_CHARACTERISTIC,        FAILED,        SUCCEEDED,    }    private ConnectionState mState = ConnectionState.IDLE;    // When this fragment is created it is given the MAC address and PIN to connect to.    public byte[] macAddress()    {        return getArguments().getByteArray("mac");    }    public int pinCode()    {        return getArguments().getInt("pin", -1);    }    // Start the connection process.    private void connectGatt()    {        // Disconnect if we are already connected.        disconnectGatt();        // Update state.        mState = ConnectionState.CONNECT_GATT;        State.notifyChanged();        BluetoothDevice device = BluetoothAdapter.getDefaultAdapter().getRemoteDevice(macAddress());        // Connect!        mGatt = device.connectGatt(getActivity(), false, mBleCallback);    }    private void disconnectGatt()    {        if (mGatt != null)        {            mGatt.disconnect();            mGatt.close();            mGatt = null;        }    }    // See https://android.googlesource.com/platform/external/bluetooth/bluedroid/+/master/stack/include/gatt_api.h    private static final int GATT_ERROR = 0x85;    private static final int GATT_AUTH_FAIL = 0x89;    private android.bluetooth.BluetoothGattCallback mBleCallback = new BluetoothGattCallback()    {        @Override        public void onConnectionStateChange(BluetoothGatt gatt, int status, int newState)        {            super.onConnectionStateChange(gatt, status, newState);            switch (newState)            {            case BluetoothProfile.STATE_CONNECTED:                // Connected to the device. Try to discover services.                if (gatt.discoverServices())                {                    // Update state.                    mState = ConnectionState.DISCOVER_SERVICES;                    State.notifyChanged();                }                else                {                    // Couldn't discover services for some reason. Fail.                    disconnectGatt();                    mState = ConnectionState.FAILED;                    State.notifyChanged();                }                break;            case BluetoothProfile.STATE_DISCONNECTED:                // If we try to discover services while bonded it seems to disconnect.                // We need to debond and rebond...                switch (mState)                {                    case IDLE:                        // Do nothing in this case.                        break;                    case CONNECT_GATT:                        // This can happen if the bond information is incorrect. Delete it and reconnect.                        deleteBondInformation(gatt.getDevice());                        connectGatt();                        break;                    case DISCOVER_SERVICES:                        // This can also happen if the bond information is incorrect. Delete it and reconnect.                        deleteBondInformation(gatt.getDevice());                        connectGatt();                        break;                    case READ_CHARACTERISTIC:                        // Disconnected while reading the characteristic. Probably just a link failure.                        gatt.close();                        mState = ConnectionState.FAILED;                        State.notifyChanged();                        break;                    case FAILED:                    case SUCCEEDED:                        // Normal disconnection.                        break;                }                break;            }        }        @Override        public void onServicesDiscovered(BluetoothGatt gatt, int status)        {            super.onServicesDiscovered(gatt, status);            // Services have been discovered. Now I try to read a characteristic that requires MitM protection.            // This triggers pairing and bonding.            BluetoothGattService nameService = gatt.getService(UUIDs.NAME_SERVICE);            if (nameService == null)            {                // Service not found.                disconnectGatt();                mState = ConnectionState.FAILED;                State.notifyChanged();                return;            }            BluetoothGattCharacteristic characteristic = nameService.getCharacteristic(UUIDs.NAME_CHARACTERISTIC);            if (characteristic == null)            {                // Characteristic not found.                disconnectGatt();                mState = ConnectionState.FAILED;                State.notifyChanged();                return;            }            // Read the characteristic.            gatt.readCharacteristic(characteristic);            mState = ConnectionState.READ_CHARACTERISTIC;            State.notifyChanged();        }        @Override        public void onCharacteristicRead(BluetoothGatt gatt, BluetoothGattCharacteristic characteristic, int status)        {            super.onCharacteristicRead(gatt, characteristic, status);            if (status == BluetoothGatt.GATT_SUCCESS)            {                // Characteristic read. Check it is the right one.                if (!UUIDs.NAME_CHARACTERISTIC.equals(characteristic.getUuid()))                {                    // Read the wrong characteristic. This shouldn't happen.                    disconnectGatt();                    mState = ConnectionState.FAILED;                    State.notifyChanged();                    return;                }                // Get the name (the characteristic I am reading just contains the device name).                byte[] value = characteristic.getValue();                if (value == null)                {                    // Hmm...                }                disconnectGatt();                mState = ConnectionState.SUCCEEDED;                State.notifyChanged();                // Success! Save it to the database or whatever...            }            else if (status == BluetoothGatt.GATT_INSUFFICIENT_AUTHENTICATION)            {                // This is where the tricky part comes                if (gatt.getDevice().getBondState() == BluetoothDevice.BOND_NONE)                {                    // Bonding required.                    // The broadcast receiver should be called.                }                else                {                    // ?                }            }            else if (status == GATT_AUTH_FAIL)            {                // This can happen because the user ignored the pairing request notification for too long.                // Or presumably if they put the wrong PIN in.                disconnectGatt();                mState = ConnectionState.FAILED;                State.notifyChanged();            }            else if (status == GATT_ERROR)            {                // I thought this happened if the bond information was wrong, but now I'm not sure.                disconnectGatt();                mState = ConnectionState.FAILED;                State.notifyChanged();            }            else            {                // That's weird.                disconnectGatt();                mState = ConnectionState.FAILED;                State.notifyChanged();            }        }    };    private final BroadcastReceiver mPairingRequestRecevier = new BroadcastReceiver()    {        @Override        public void onReceive(Context context, Intent intent)        {            if (BluetoothDevice.ACTION_PAIRING_REQUEST.equals(intent.getAction()))            {                final BluetoothDevice device = intent.getParcelableExtra(BluetoothDevice.EXTRA_DEVICE);                int type = intent.getIntExtra(BluetoothDevice.EXTRA_PAIRING_VARIANT, BluetoothDevice.ERROR);                if (type == BluetoothDevice.PAIRING_VARIANT_PIN)                {                    device.setPin(Util.IntToPasskey(pinCode()));                    abortBroadcast();                }                else                {                    L.w("Unexpected pairing type: " + type);                }            }        }    };    public static void deleteBondInformation(BluetoothDevice device)    {        try        {            // FFS Google, just unhide the method.            Method m = device.getClass().getMethod("removeBond", (Class[]) null);            m.invoke(device, (Object[]) null);        }        catch (Exception e)        {            L.e(e.getMessage());        }    }}

I also faced the same problem and after all the research, I figured out the below solution to pair to a BLE without any manual intervention.

(Tested and working!!!)

I am basically looking for a particular Bluetooth device (I know MAC address) and pair with it once found. The first thing to do is to create pair request using a broadcast receiver and handle the request as below.

IntentFilter intentFilter = new IntentFilter(BluetoothDevice.ACTION_PAIRING_REQUEST);                intentFilter.setPriority(IntentFilter.SYSTEM_HIGH_PRIORITY);                registerReceiver(broadCastReceiver,intentFilter);

You need to write the broadcastReceiver and handle it as below.

String BLE_PIN = "1234"private BroadcastReceiver broadCastReceiver = new BroadcastReceiver() {    @Override    public void onReceive(Context context, Intent intent) {        String action = intent.getAction();        if(BluetoothDevice.ACTION_PAIRING_REQUEST.equals(action))        {            BluetoothDevice bluetoothDevice = intent.getParcelableExtra(BluetoothDevice.EXTRA_DEVICE);            bluetoothDevice.setPin(BLE_PIN.getBytes());            Log.e(TAG,"Auto-entering pin: " + BLE_PIN);            bluetoothDevice.createBond();            Log.e(TAG,"pin entered and request sent...");        }    }};

Voila! You should be able to pair to Bluetooth device without ANY MANUAL INTERVENTION.

Hope this helps :-) Please make it right answer if it works for you.