The success of chemotherapy regimens has led to an increase in cancer survival rate over the last decades. Melphalan has been widely used for the treatment of several types of cancers despite its gonadotoxic effects. Due to its ability to cause mutations in the spermatogonial stem cells and spermatids, melphalan can exert a negative impact on male reproductive health in young cancer survivors. β‐aminoisobutyric acid (BAIBA), a myokine released by skeletal muscles, has been reported to have beneficial effects in diabetic nephropathy, cardiomyopathy and hepatic toxicity. However, the exact role of BAIBA in chemotherapy‐induced germ cell toxicity is still unexplored. The present study aims to determine the dose‐dependent (25, 50, and 100 mg/kg) effects of BAIBA on melphalan‐induced (1.5 mg/kg) germ cell toxicity in sprague−dawley (SD) rats. The evaluation parameters included quantification of oxidative stress biomarkers, sperm count, sperm motility and head morphology, sperm and testicular DNA damage, sperm mitochondrial membrane potential, ultrastructural changes in sperms, histological and protein expression studies in testes. Melphalan treatment significantly altered all the above‐mentioned parameters and the high dose (100 mg/kg) of BAIBA restored melphalan‐induced toxicity in a significant manner by exerting antioxidant, anti‐inflammatory and antiapoptotic effects. However, the medium dose (50 mg/kg) of BAIBA decreased the toxicity of melphalan and the low dose (25 mg/kg) of BAIBA failed to counteract the melphalan‐induced male germ cell toxicity as well as the peripheral blood micronucleus induction. The antioxidant, anti‐inflammatory and antiapoptotic role of BAIBA in melphalan‐induced gonadal damage is a novel finding in an experimental rat model.