Abstract The main aim of this paper is to give the definitions of Caputo fractional derivative operators and show their use in the special function theory. For this purpose, we introduce new types of incomplete hypergeometric functions and obtain their integral representations. Furthermore, we define incomplete Caputo fractional derivative operators and show that the images of some elementary functions under the action of incomplete Caputo fractional operators give a new type of incomplete hypergeometric functions. This definition helps us to obtain linear and bilinear generating relations for the new type incomplete Gauss hypergeometric functions.