Purpose: The purpose of this study is to investigate the relationship between physical fitness (PF) level and Chinese middle-school students’ perceived well-being, motivation, and enjoyment. Method: In this study, the participants were randomly selected from 16 Beijing-based middle schools in China. In addition to the collection of demographic data (i.e., gender, age, and parental education), tools including the Warwick-Edinburgh Mental Well-Being Scale, the Behavioural Regulation in Sport Questionnaire, and the Physical Activity Children’s Enjoyment Scale were employed for collecting data on other variables of well-being, motivation, and enjoyment, respectively. Results: A total of 1678 adolescents (M age = 14.66 years, SD = 1.80) participated in this study. According to the results, significant gender differences could be observed in the PF categories of mean age, BMI, vital capacity, 50-m sprint, muscular strength, and flexibility (all p < 0.05). In contrast, there was no significant gender difference in the levels of well-being, motivation, and enjoyment observed, with similar scores for boys and girls (p > 0.05). Indeed, adolescents with low BMI scores and high levels of vital capacity, muscular strength, and flexibility showed better well-being, motivation, and enjoyment. However, no association was observed between timed sit-ups and pull-ups and well-being, motivation, and enjoyment. Conclusions: This study produced preliminary findings on the relationship between PF and Chinese adolescents’ perceived well-being, motivation, and enjoyment. To improve the health of adolescents, it is necessary to adopt prospective and experimental research designs for advocating for fitness education in school-based programs in future research.