A farmer's son from New York State, Babcock gained his AB degree from Tufts College, Massachusetts, in 1866 and after a period of farming became a chemistry assistant and (from 1875) instructor at Cornell University. In 1879 he gained his doctorate under Hans Hübner at Göttingen, Germany. After a further spell at Cornell on his return, he became chemist at the New York Agricultural Station in 1882, where he worked on the analysis of milk.

In 1888 Babcock became professor of agricultural chemistry at the University of Wisconsin. Here, in 1890, he devised an efficient test (the Babcock test), which quickly became standard, for measuring the butterfat content of milk. Studies followed on rennet, fermentation, metabolic water, and animal nutrition. In 1907 Babcock's associates began studies in which cattle were fed balanced diets derived from a single source – corn, wheat, or oats. The results obtained provided further evidence for the existence of accessory food factors and Babcock's school played an important part in the vitamin studies that followed.