At present, there are several synthetic medications for toxoplasmosis therapy; however, these agents cannot be permanently applied because of adverse side effects or therapeutic failures and drug resistance in parasites. The present experimental investigation was aimed to study the effects of royal jelly (RJ) obtained from Apis mellifera in comparison with atovaquone against Toxoplasma gondii infection in mice. After treatment of infected mice with RJ at the doses of 200, 400, and 600 mg/kg for 14 consecutive days, we evaluated the therapeutic activity of RJ by measuring the mean number and the mean size of T. gondii tissue cysts, oxidant-antioxidant enzymes, pro-inflammatory cytokines, the mRNA expression levels of bradyzoite surface antigen 1 (BAG1), as well as the toxic effect on liver and kidney function. Treatment of the infected mice with RJ significantly (p < 0.001) decreased the mean number and the mean diameter of T. gondii tissue cysts and downregulated BAG1 in a dose-dependent response. After treatment of infected mice with RJ, the level of oxidative stress markers was significantly diminished, but a significant increase (p < 0.05) in the level of antioxidant markers such as glutathione peroxidase (GPx) and superoxide dismutase (SOD) enzymes was observed. Treatment of the infected mice with RJ significantly enhanced the level of pro-inflammatory cytokines IFN-γ and IL-1β, whereas it caused no substantial change in the serum levels of liver and kidney enzymes. The findings of this in vivo study revealed the favorable therapeutic effect of RJ on latent T. gondii infection in mice. It was found that RJ considerably inhibited the infection by decreasing the number and size of tissue cysts, reducing oxidative stress, and boosting the level of pro-inflammatory cytokines, but had no significant toxic impact on the function of vital organs such as liver and kidney. However, additional surveys are required to confirm these findings and clarify the exact mechanisms and their efficiency in clinical subjects.