I once used astrophotography tool DeepSkyStacker for that.

Loaded all my photos as light frames, prepared and loaded a dark frame, turned off alignement, post-processing etc and turned on "Create a calibrated file for each light frame". It subtracted given dark frame from every photo and exported them to 16-bit TIFFs.

It can be used from command line if you want to automate it more or make custom GUI. Windows only unfortunately, but it is open source.