Install pandoc using the Windows installer from here. Install pandoc globally using this command (using the path to the version of pandoc you downloaded):
msiexec /i pandoc-1.12.3.msi ALLUSERS=1
Install miktex from here.
Run these commands to check that pandoc and miktex are installed:
"C:\Program Files (x86)\Pandoc\pandoc.exe" --version
"C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\pdflatex.exe" --version
Usage
Markdown to html example:
pandoc path/to/Some.md -o Some.html