The fungicide iprodione (IPR) and the insecticide chlorpyrifos (CPF) are concurrently applied for early disease control in fruits and other crops. However, there are no available data about the impacts of their co-exposure. Additionally, IPR and CPF are known as endocrine disruptors that can cause reproductive toxicity. The outcomes of their co-exposure on the development of male reproductive organs are still unknown. Therefore, this study aimed to assess the risk of exposure to these pesticides, particularly on the postnatal development of the male albino rat reproductive system from postnatal days 23–60. The results revealed that a single IPR or CPF exposure has harmful consequences on the reproductive development and function manifested by reduced testicular weight, serious changes in sperm characteristics, reproductive hormone level imbalance, testicular enzymes, oxidative stress and apoptosis-related enzymes, which correlated with transcription levels of steroidogenic- and spermatogenic- related genes. Histopathologically, both compounds caused severe damage in the testis and accessory glands architecture. Notably, co-exposure to IPR and CPF in rats caused more serious damage, indicative of an additive effect than individual exposure, so concurrent exposure should be avoided as it is more hazardous, especially on male fertility.