The Berry phase is an important concept in solids, correlated to the band topology, axion electrodynamics, and potential applications of topological materials. Here, we investigate the magnetotransport and Berry phase of rare earth element Gd-doped Bi2Se3 (Gd:Bi2Se3) topological insulators (TIs) at low temperatures and high magnetic fields. Gd:Bi2Se3 single crystals show Shubnikov-de Haas (SdH) oscillations with nontrivial Berry phase, while Bi2Se3 single crystals show zero Berry phase in SdH oscillations. A fitting of the temperature-dependent magnetization curves using the Curie-Weiss law reveals that the Gd dopants in the crystals show paramagnetism in the 3-300 K region, indicating that the origin of the Berry phase is not long-range magnetic ordering. Moreover, Gd doping has limited influence on the quantum oscillation parameters (e.g., frequency of oscillation, area of Fermi surface, effective electron mass, and Fermi wave vectors) but has a significant impact on the Hall mobility, carrier density, and band topology. Our results demonstrate that Gd doping can tune the Berry phase of TIs effectively, which may pave the way for the future realization of many predicted exotic transport phenomena of topological origin.