Salt stress severely reduces growth and yield of plants. Considering the positive effects of selenium (Se) and chitosan (Cs) separately against abiotic stress, in these experiments, we synthesized chitosan–selenium nanoparticles (Cs–Se NPs) and investigated their ability to reduce the negative effects of salt stress on growth and some biochemical parameters of bitter melon (Momordica charantia). Bitter melon plants were grown at three NaCl salinity levels (0, 50, and 100 mM) and a foliar spray of Cs–Se NPs (0, 10, and 20 mg L−1) was applied. Some key morphological, biochemical, and physiological parameters in leaf samples and essential oil from fruit were measured at harvest. Salinity decreased growth and yield while foliar application of Cs–Se NPs increased these critical parameters. Furthermore, Cs–Se NPs enhanced bitter melon tolerance to salinity by increasing antioxidant enzyme activity, proline concentration, relative water content, and K+, and decreasing MDA and H2O2 oxidants and Na aggregation in plant tissues. Yield was also improved, as the highest amount of essential oils was produced by plants treated with Cs–Se NPs. Generally, the greatest improvement in measured parameters under saline conditions was obtained by treating plants with 20 mg L−1 Cs–Se NPs, which significantly increased salinity tolerance in bitter melon plants.