After graduating, he immediately began work with the United States Bureau of Biological Survey in Kansas and North Dakota.

He served in the Army in France during World War I, but still found time to collect specimens which he sent back to Berkeley and the University of Kansas.

In 1921 he became assistant biologist for the Biological Survey based in Washington, and worked there for the next eight years, concerned chiefly with studying toads and the feeding habits of hawks and owls.

Merriam encouraged Kellogg to use his free time to study the fossilized marine mammals of Calvert Cliffs in Maryland.

At the museum he devoted time to studying the Archaeoceti, primitive whales from the Eocene and early Oligocene, and the Miocene Cetacea of North America.

He retired from his posts at the Smithsonian in 1962, but continued to work on his study of Miocene Cetacea, publishing nine papers on fossil marine mammals between 1965 and 1969.