Felipe, you mean the builtin python window I presume
Any script or script tools you run while inside Desktop honors the background processing setting. If background processing is turned on, the scripts will execute in the 64-bit space.
Background Geoprocessing (64-bit)—Help | ArcGIS for Desktop
If it is external then you need to ensure that the correct python is executing.
You can use
import sys
sys.executable
to ensure that c:\Python27\ArcGISx6410.2\python.exe is the running version.
Alternately... use Pro, it is 64 bit