The pharmacy is the room where the medications and other chemicals used at the 4077th MASH are kept.
The rare scenes we have of the pharmacy show that it is small room with shelves full of medicines in bottles. There is also a working table with equipment such as a mortar and pestle for the preparation of mediations. Although it looks very much like the more frequently seen lab, there is ample evidence that it is actually a separate facility. In Season 5 "Bug Out", Potter tells Frank that the MASH facilities are to be loaded in the following sequence: "One, pharmacy; two, lab; three, X-ray; four, pre-op; five, O.R..." The pharmacy is given top priority probably because it holds sensitive or expensive medications.
The pharmacy is normally under the charge of a pharmacy technician, such as Sergeant Glassberg who appears in Season 6 "Major Topper". In that episode, the 4077th has run out of painkillers, so Hawkeye and B.J. are sent to the pharmacy to make up "50 little white lies"--placebos. But to do that, Hawkeye and B.J. must first get rid of Glassberg, who is on duty in the pharmacy.
In Season 7 "Dear Comrade", Potter and Hawkeye try to make some ointment for the strange rash which is affecting many of their patients. It is likely that the scene of them doing this is in the pharmacy, which is the natural place for such an activity. However, just before that scene, Potter says, "We got a lab, equipment. We're supposed to have brains. Let's use 'em, come up with an answer."