"Tony" Pirie was remarkable in sustaining two careers, one as a biochemist and the other as an educator, working on malnutrition. Both careers were committed to the prevention of blinding eye disease.

At the outbreak of war she was seconded to work with Ida Mann on the responses of the eye to war gases. After the war she joined Ida Mann as a research assistant at the newly-built Nuffield Laboratory of Ophthalmology, where they were engaged in the problems of ocular development, metabolism and toxicology. In 1946 they wrote "The Science of Seeing" partly to refute Aldous Huxley's 'pernicious" book The Art of Seeing .

In 1947 Tony Pirie became Margaret Ogilvie's reader in ophthalmology and was elected to a professorial fellowship at Somerville College. This was the beginning of a period of exciting and innovative research that covered the broad fields of Ophthalmic Biochemistry. Her later research was directed almost exclusively to the lens and cataract. She made fundamental discoveries in the areas of lens metabolism, enzymes and lens proteins.

She was the first to characterise vitreous collagen. Many of her studies have concerned themselves with the characterisation of lens crystallins and the changes in crystallins occurring in cataract. She was fascinated by vitamins and their importance in eye tissues. She was one of the leaders actively involved in seeking ways to prevent and alleviate vitamin A deficiency in developing countries.