Variation in vector traits can modulate local scale differences in pathogen transmission. Here, we compared seasonal variation in the wing length (proxy for body size) and energy reserves of adult wild-caught Aedes aegypti populations from a dengue endemic (Kilifi) and non-endemic (Isiolo) area of Kenya. Vector sampling in the dengue endemic site was conducted during the dry and wet seasons. In the non-endemic area, it was limited to the dry season which characterizes this ecology where sporadic or no rainfall is commonplace during the year. We found variation by site in the body size of both sexes, with an overall smaller size of Ae. aegypti populations collected from Isiolo than those from Kilifi. Our results show that although total carbohydrates and lipids levels were highest in both sexes during the dry season, they were two-fold higher in males than females. However, we found weak correlations between body size and energy reserves for both sexes, with body size being more sensitive in identifying differences at a population level. These results provide insights into the determinants of the vectoring potential of Ae. aegypti populations in dengue endemic and non-endemic ecologies in Kenya.