Near-infrared (NIR) persistent luminescence (PersL) materials have unique optical properties with promising applications in bioimaging and anticounterfeiting. However, their development is currently hindered by poor red-light-exciting ability. In this study, CaTiO3:Cr0.001,Y0.02 (CTCY) was synthesized with 650 nm-excited 772 nm NIR PersL. The Y3+ doping in the Ca2+ lattice plays a key role in the PersL property. A charge compensation mechanism was proposed, in which Cr3+ in the Ti4+ lattice was stabilized by Y3+-doping while oxygen vacancies were generated to store the excitation energy at the same time. A thermal ionization mechanism might elucidate the red-light-excited NIR PersL of CTCY, which benefits from the perovskite structure of CaTiO3. CTCY has 120 times more intense red-light-excited PersL than Zn3Ga2Ge2O10:Cr. Its potential applications in luminescence anticounterfeiting and bioimaging were demonstrated using a visible/NIR dual-channel PersL flower painting and a CTCY-labeled bone screw for in situ reactivable PersL imaging using red light illumination instead of X-ray, respectively. This study not only provides a new NIR PersL material but also will add to our understanding in developing other potential red-light- or even NIR-activable PersL materials with perovskite-like structures.