In this work, we analyze the rare decays of the neutral vector mesons $J/\psi$ and $\Upsilon(nS)$ in the scenario of the minimal R-symmetric supersymmetric standard model by means of the effective Lagrangian method. The predicted branching ratios are dominated by the mass insertion parameters $\delta^{ij}$, i.e., the off-diagonal inputs, and the contributions from different parts are comparable. Taking account of the constraints on the mass insertion parameters by the experiments, the predicted branching ratios for the most promising processes $\Upsilon(nS)\rightarrow l\tau$ are ten orders of magnitude smaller than the present experimental bounds.Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Article funded by SCOAP3 and published under licence by Chinese Physical Society and the Institute of High Energy Physics of the Chinese Academy of Science and the Institute of Modern Physics of the Chinese Academy of Sciences and IOP Publishing Ltd.