Abstract This work investigates the annealing effects on the superconducting properties of FeTe0.65Se0.35 single crystals. We examine the impact of varying annealing times on the magnetotransport, magnetic, and vortex pinning properties of the single crystals. The structural analysis shows the single crystalline growth of crystals along the c-axis. X-ray photoelectron spectroscopy results confirm the presence of iron oxides in the annealed samples. Temperature-dependent resistivity and magnetization measurements confirm the superconductivity in the as-grown and annealed samples. However, the as-grown sample shows a broad superconducting transition and low superconducting volume fraction, but after annealing, significant improvement in both is observed. Moreover, the self-field critical current density at 2 K is enhanced by a factor of ~4.5 for the optimally annealed sample compared to the as-grown sample. Experimental observations have been analyzed with the theoretical models to understand the effects of annealing on the vortex pinning mechanisms. Further, the specific heat study confirms the bulk superconductivity in the annealed sample compared to the as-grown single crystal. Overall, our study indicates that the superconducting properties vary with the annealing time, and the best results are obtained at an optimum annealing time.