Ocean warming and acidification are climate change related drivers that impact the physiology of marine organisms, affecting their coping ability to future environments. In addition, marine ecosystems are also facing pollution from an ever-growing diversity of chemical contaminants, including endocrine disruptors. A common example is the 17α-ethynylestradiol (EE2), which can affect the endocrine regulation of fish and hence potentially impacting their fitness. Thus, fish have to cope to multiple climatic and chemical stresses that can interact, influencing the overall impact on fish physiology. In this study, we investigated whether the impacts of early exposure to EE2 (15 ng.L-1; one month during embryo-larval development) on survival, growth and reproductive axis of prepubertal sticklebacks is modulated by the RCP8.5 scenario (+3°C; -0.4 pH unit) after five months post-contamination. Fish used in this study were offspring of parents that had previously acclimated to identical climatic scenario, providing a baseline for understanding the potential interplay between endocrine disruptor exposure and projected climate change scenario. Our findings revealed that the survival of juveniles, when exposed to EE2 during early development, is reduced under Current but not RCP8.5 scenario. Furthermore, under RCP8.5-EE2, a significantly lower body length was observed. The study highlighted sex and tissue specific responses, regarding expression profiles of genes related with development and sexual maturation. Interestingly, the expression of ovarian aromatase (cyp19a1a) showed a significant interaction between RCP8.5 and EE2, suggesting a long-lasting estrogenic effect under RCP8.5 scenario. Additionally, skewed sex ratios and the presence of intersex individuals in both scenarios suggested feminization due to EE2, potentially disrupting sexual maturation and future reproduction. Hence, the early EE2 exposure had long-term physiological effects on sticklebacks, and these effects can be modulated by the climate scenario. This underscores the importance undertaking multiparametric and long-term studies to comprehensively understand the vulnerability on fish population in future environments.