The Fairbanks Museum holds the largest and most comprehensive collection of New England fauna and flora in a museum north of Boston. The Museum houses a comprehensive collection of New England mammals and birds, with most native species represented, plus noteworthy collections of North American fauna. Additionally, the Museum houses the Vermont State Geologic Collection, and a noteworthy herbarium of New England plants.

As a result of founder Franklin Fairbanks' passion for nature, especially birds, the Museum also possesses an extraordinary selection of birds from around the globe, totaling over 3,000 specimens of nearly 1,000 species. Fairbanks's travels stimulated other noteworthy citizens of Vermont to donate their own personal collections of objects.

Today, the Museum holds significant collections of rocks and minerals, gems, shells, corals, butterflies, Arctic insects, New England bird nests and egg sets, and one of the world's most diverse collections of mounted hummingbirds.