The Department of Ophthalmology was established on 16 June 1965. This department is a  tertiary care Ophthalmic Centre which caters to the training of undergraduates, post graduates, nursing cadets & paramedical ophthalmic staff. The post graduate residency programme is elaborate and training is imparted in various sub-specialities including cornea, glaucoma, retina, squint, oculoplasty and cataract. The vitreo-retinal centre of this department caters to all vitreo-retinal cases of Southern Command and civilians in Pune and various parts of Maharashtra. It has been in the forefront of conducting trial of intra-vitreal injection of anti-VEGFs in age related macular degeneration and other retinal disorders. Regular diagnostic and surgical eye camps with free foldable intra ocular lens implantation are carried out in which the undergraduates and postgraduates actively participate. The department is actively involved in conducting annual workshops in retina, fundus  fluorescein angiography and age related macular degeneration which are highly appreciated by the faculty and post graduate students from surrounding medical colleges.

Eye bank:

The department has a registered Eye Bank and corneal transplantation is done for the corneal blind. This is amongst the only centres in Pune treating high risk keratoplasty patients with Mycophenolate mofetil with good visual rehabilitation of the visually impaired people.
Various activities  are carried out during  the Cornea donation Fortnight like lectures, posters  , messages in cinema houses .An annual Inter-collegiate quiz for under-graduates is  also held regularly during this fortnight amongst the local Medical colleges of Pune. This has raised awareness of eye donation amongst undergraduate students, nursing staff. Glaucoma awareness and diagnostic camps are held annually during the Glaucoma Week. This center is amongst the very few centers in Pune where Ahmed Glaucoma Valve implant surgery is being done for refractory types of glaucoma. The department regularly organizes CMEs and updates at local and at National level. Some of the notable conferences held at AFMC in the year 2010 include; Recent advances in ophthalmology and perspectives for the AFMS, Neuro ophthalmology update, instructional course on automated perimetry and a seminar on Anti VEGFs in AMD. Residents actively participate in presenting interesting cases in the Poona Ophthalmological Society monthly and annual meetings. The department is a recognized centre for conducting the DNB examinations and imparts training to the DNB candidates during mock examinations.