Background: This study aimed to investigate the association of elementary school students’ manipulative skill competency, cardiorespiratory fitness, and cognitive function with psychological wellbeing (PWB), as well as whether the association had gender differences. Methods: Participants were 291 fourth-grade students (166 boys vs. 125 girls; mean age = 9.770 years old; SD = 0.584) at two elementary schools from the province of Henan in China. The students’ soccer skills in manipulative skill competency were assessed using the PE Metric Assessment Rubric, cardiorespiratory fitness was assessed by means of the PACER 15 m test, and cognitive function and PWB were assessed using the d2 test of attention and Warwick–Edinburgh Mental Wellbeing Scale, respectively. Data were analyzed with descriptive statistics and multiple linear regression models. Results: The result of linear regression models showed that soccer skills, cardiorespiratory fitness, and cognitive function were collectively associated with PWB for the total sample (F (5, 285) = 3.097, p < 0.01), boys (F (5, 160) = 1.355, p < 0.01), and girls (F (5, 119) = 2.132, p < 0.01). Furthermore, the standardized regression coefficients (β) indicated that cardiorespiratory fitness was the only significant contributor to PWB for the total sample (β = 0.119, t = 2.021, p < 0.05), but not for boys and girls. Soccer skills and cognitive function were not individual significant contributors to PWB for the total sample, boys, and girls. Conclusions: Cardiorespiratory fitness was significantly associated with PWB, and there were no gender differences in the relationship of manipulative skill competency, cardiorespiratory fitness, and cognitive function with PWB in elementary school students. This study provides empirical evidence that improving cardiorespiratory fitness is an important intervention strategy to promote elementary school students’ PWB.