A potential association between pet ownership and mental well-being is suggested, but there is a shortage of high-quality longitudinal studies that consider probable differences among different species. We aimed to examine whether ownership of the most popular pets (dogs and cats) would predict mental well-being. The Tokyo Teen Cohort (TTC), a prospective population-based birth cohort study, had dog and cat ownership data at age 10 and mental well-being score at ages 10 and 12 from 2584 adolescents. Linear regression analysis with adjusting for covariates showed that dog ownership had a positive effect on mental well-being compared to no dog ownership, however, cat ownership had a negative effect compared to no cat ownership. Two-factor mixed-design analysis of variance showed that dog ownership predicted maintained mental well-being, while cat ownership predicted progressing decline of mental well-being. Thus, dog and cat ownership may have different effects on adolescents’ mental well-being, implying that the underlying mechanisms that are activated by these types of ownership may differ.