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Toxoplasmosis is a disease that causes high mortality in immunocompromised individuals, such as AIDS patients, and sequelae in congenitally infected newborns. Despite its great medical importance, there are few treatments available and these are associated with adverse events and resistance. In this work, after screening the drugs present in the Medicines for Malaria Venture Pandemic Box, we found new hits with anti-Toxoplasma gondii activity. Through our analysis, we selected twenty-three drugs or drug-like compounds that inhibited the proliferation of T. gondii tachyzoites in vitro by more than 50% at a concentration of 1 µM after seven days of treatment. Nineteen of these compounds have never been reported active before against T. gondii. Inhibitory curves showed that most of these drugs were able to inhibit parasite replication with IC50 values on the nanomolar scale. To better understand the unprecedented effect of seven compounds against T. gondii tachyzoites, an ultrastructural analysis was carried out using transmission electron microscopy. Treatment with 0.25 µM verdinexor, 3 nM MMV1580844, and 0.25 µM MMV019724 induced extensive vacuolization, complete ultrastructural disorganization, and lytic effects in the parasite, respectively, and all of them showed alterations in the division process. Treatment with 1 µM Eberconazole, 0.5 µM MMV1593541, 1 µM MMV642550, 1 µM RWJ-67657, and 1 µM URMC-099-C also caused extensive vacuolization in the parasite. The activity of these drugs against intracellular tachyzoites supports the idea that the drugs selected in the Pandemic Box could be potential future drugs for the treatment of acute toxoplasmosis.