Deep levels in GaAs on Si substrates grown by metalorganic chemical vapor deposition (MOCVD) were studied during infrared rapid thermal annealing. For GaAs layers on Si after annealing at 850 °C for 20 s, three electron deep levels at 0.36, 0.27, and 0.20 eV below the conduction band were created as the dominant deep levels. Especially, the 0.36 eV level was found to increase up to 40% of the donor concentration as the thickness of Si substrates increased. These results indicate that rapid thermal annealing of GaAs on Si may induce high‐density deep levels due to a biaxial tensile stress caused by the difference in thermal expansion coefficients.