To examine the associations of self-perceived and objectively-measured physical fitness with psychological well-being and distress indicators in young pediatric cancer survivors. A total of 116 participants (12.1 ± 3.3 years, 56.9% boys) from the iBoneFIT project participated in this cross-sectional study. Objectively-measured physical fitness (muscular fitness) was obtained by handgrip strength and standing long jump tests for the upper and lower body, respectively. Self-perceived physical fitness was obtained by the International Fitness Scale (IFIS). Positive and negative affect were assessed by the positive affect schedule for children (PANAS-C), happiness by Subjective Happiness Scale (SHS), optimism by Life Orientation Test-Revised (LOT-R), self-esteem by the Rosenberg Self-Esteem Scale (RSE), anxiety by State-Trait Anxiety Inventory for Children (STAIC-R), and depression by Children Depression Inventory (CDI). Multiple linear regressions adjusted by key covariates were performed to analyze associations. No associations were found between objectively-measured muscular fitness and any of the psychological well-being and distress indicators (p > 0.05). Self-perceived overall fitness and flexibility were positively associated with positive affect (β ≥ 0.258, p < 0.05). Self-perceived cardiorespiratory fitness, speed/agility, and flexibility were negatively associated with depression (β ≥ -0.222, p < 0.05). Finally, self-perceived cardiorespiratory fitness was also negatively associated with anxiety and negative affect (β ≥ -0.264, p < 0.05). Perceived physical fitness, but not objectively physical fitness, seems to be inversely related to psychological distress variables and to less extent positively related to psychological well-being. The findings from this study highlight the importance of promoting self-perceived fitness in the pediatric oncology population.