Electronic waste management is a global rising concern that is primarily being handled by informal recycling practices. These release a mix of potentially hazardous chemicals, which is an important public health concern. These chemicals include polybrominated diphenyl ethers (PBDEs), used as flame retardants in electronic parts, which are persistent in nature and show bioaccumulative characteristics. Although PBDEs are suspected endocrine disruptors, particularly targeting thyroid and reproductive hormone functions, the relationship of PBDEs with these health effects are not well established. We used the Navigation Guide methodology to conduct a systematic review of studies in populations exposed to e-waste to better understand the relationships of these persistent flame retardants with hormonal and reproductive health. We assessed nineteen studies that fit our pre-determined inclusion criteria for risk of bias, indirectness, inconsistency, imprecision, and other criteria that helped rate the overall evidence for its quality and strength of evidence. The studies suggest PBDEs may have an adverse effect on thyroid hormones, reproductive hormones, semen quality, and neonatal health. However, more research is required to establish a relationship of these effects in the e-waste-exposed population. We identified the limitations of the data available and made recommendations for future scientific work.