Josef Flammer (born April 21, 1948) is a Swiss ophthalmologist and long-time director of the Eye Clinic at Basel University Hospital.

Flammer is a glaucoma specialist who developed a new pathogenetic concept of glaucomatous damage according to which unstable blood supply leads to oxidative stress, which in turn plays a major role in apoptosis (cell death) of cells in the optic nerve and retina in glaucoma patients.

Flammer was one of the first researchers to demonstrate systemic side effects of locally administered beta blockers (i.e. eye drops) in ophthalmology.

In numerous research projects he demonstrated that glaucoma could be caused by a dysregulation of ocular blood flow, even at normal levels of intraocular pressure.

Later, he noted that such spasms are only the tip of the iceberg and an indication of a much more generalized vascular dysregulation in the human body.