Along with recent advancements in thin-film technologies, the engineering of complex transition metal oxide heterostructures offers the possibility of creating novel and tunable multifunctionalities. A representative complex oxide is the perovskite strontium titanate (STO), whose bulk form is nominally a centrosymmetric paraelectric band insulator. By tuning the electron doping, chemical stoichiometry, strain, and charge defects of STO, it is possible to control the electrical, magnetic, and thermal properties of such structures. Here, we demonstrate tunable magnetism in atomically engineered STO thin films grown on STO (001) substrates by controlling the atomic charge defects of titanium (V_Ti) and oxygen (V_O) vacancies. Our results show that the magnetism can be tuned by altering the growth conditions. We provide deep insights into its association to the following defect types: (i) V_Ti, resulting in a charge rearrangement and local spin polarization, (ii) V_O, leading to weak magnetization, and (iii) V_Ti–V_O pairs, which lead to the appearance of a sizable magnetic signal. Our results suggest that controlling charged defects is critical for inducing a net magnetization in STO films. This work provides a crucial step for designing magnetic STO films via defect engineering for magnetic and spin-based electronic applications.