The model of severe poisoning with acetylcholinesterase inhibitors has shown the possibility of drug treatment of toxic effects with valproic acid containing a tertiary amino group. The study was aimed to assess potential mutagenic effects of the valproic acid derivative containing a tertiary amino group when studing its safety. Testing for toxicophores and assessment of the mutagenic effect probability were perfomed using the QSAR Toolbox offline software (v4.5 SP1). The Ames test with and without metabolic activation was used to estimate mutagenic potential of valproic acid containing a tertiary amino group in vitro. The computer prediction results predicted that the test substance would show no mutagenic effects in the Ames test. These data were confirmed by the in vitro Ames test for a broad range of concentrations of valproic acid containing a tertiary amino group (0.02–5.0 mg/mL). The concentrations of valproic acid containing a tertiary amino group exceeding 1.58 mg/mL have a bacteriostatic effect on the TA 100 S. typhimurium strain and the WP2 uvr A pKM 101с E. coli strain. Thus, the valproic acid derivative containing a tertiary amino group possesses no mutagenic effect, it can be recommended for further preclinical trials of therapeutic efficacy and safety.