How do I install SciPy on 64 bit Windows?

Unofficial 64-bit installers for NumPy and SciPy are available at http://www.lfd.uci.edu/~gohlke/pythonlibs/

Make sure that you download & install the packages (aka. wheels) that match your CPython version and bitness (ie. cp35 = Python v3.5; win_amd64 = x86_64).

You'll want to install NumPy first; From a CMD prompt with administrator privileges for a system-wide (aka. Program Files) install:

C:\>pip install numpy‑<version>+mkl‑cp<ver-spec>‑cp<ver-spec>m‑<cpu-build>.whl

Or include the --user flag to install to the current user's application folder (Typically %APPDATA%\Python on Windows) from a non-admin CMD prompt:

C:\>pip install --user numpy‑<version>+mkl‑cp<ver-spec>‑cp<ver-spec>m‑<cpu-build>.whl

Then do the same for SciPy:

C:\>pip install [--user] scipy‑<version>‑cp<ver-spec>‑cp<ver-spec>m‑<cpu-build>.whl

Don't forget to replace <version>, <ver-spec>, and <cpu-build> appropriately if you copy & paste any of these examples. And also that you must use the numpy & scipy packages from the ifd.uci.edu link above (or else you will get errors if you try to mix & match incompatible packages -- uninstall any conflicting packages first [ie. pip list]).

Short answer: Windows 64 bit support is still work in progress at this time. The superpack will certainly not work on a 64-bits Python (but it should work fine on a 32 bits Python, even on Windows 64 bit).

The main issue with Windows 64 bit is that building with mingw-w64 is not stable at this point: it may be our's (NumPy developers) fault, Python's fault or mingw-w64. Most likely a combination of all those :). So you have to use proprietary compilers: anything other than the Microsoft compiler crashes NumPy randomly; for the Fortran compiler, ifort is the one to use. As of today, both NumPy and SciPy source code can be compiled with Visual Studio 2008 and ifort (all tests passing), but building it is still quite a pain, and not well supported by the NumPy build infrastructure.

As the transcript for SciPy told you, SciPy isn't really supposed to work on Win64:

Warning: Windows 64 bits support is experimental, and only available fortesting. You are advised not to use it for production.

So I would suggest to install the 32-bit version of Python, and stop attempting to build SciPy yourself. If you still want to try anyway, you first need to compile BLAS and LAPACK, as PiotrLegnica says. See the transcript for the places where it was looking for compiled versions of these libraries.