Ce‐doped yttrium aluminum garnet (YAG) is among the efficient rare‐earth garnet scintillators and phosphors. Herein, a computational and experimental study of complex F‐type defect centers formed in YAG by doping with cerium and carbon is addressed. The formation energies determined by ab initio calculations of different defects and atomic chemical potentials in YAG:Ce,C are discussed in O‐poor and O‐rich conditions corresponding to the crystal growth under Ar+CO reducing atmosphere, and postgrowth annealing in air, respectively. It is shown that as‐grown crystals contain numerous positively charged defects responsible for F‐type center formation, whereas mainly negative‐charged defects are remained after the annealing in air. The negatively charged defects located nearby Ce luminescence center occupying Y site may stabilize cerium in the tetravalent state and promote a hole transport to this luminescence center. This describes a high scintillation efficiency of Ce,C‐doped garnets. Furthermore, YAG:C and YAG:Ce,C with a high carbon concentration, in addition to luminescence peaked at 400 ns ascribed to F+‐type centers, possess a fast luminescence peaked around 650 nm that may be attributed to the complex defect centers. These unveiled features of the luminescence process in rare‐earth garnets may contribute to the development of efficient luminescence materials.