The worldwide increase in childhood overweight and obesity underscores the need to study variables like fundamental movement skill (FMS) levels from early childhood. This study investigated the bidirectional longitudinal relationship between body mass index (BMI) and process-oriented FMSs, including locomotor skills and object control skills in 675 Finnish children, aged 3–8 years at baseline (50.5% female, mean age 5.5 years) over 3 years. Standardized BMI-for-age SD scores (BMI SDS z-scores) followed Finnish national standards. The FMS assessment comprised four subtests from the Test of Gross Motor Development, third edition. Age-adjusted standardized residuals of FMS or skill domains and BMI SDS z-scores were used in a two-level, cross-classified, cross-lagged regression analysis, accounting for gender, and baseline value of the dependent variables. The results showed no statistically significant longitudinal relationship between BMI and FMS or its skill domains for either gender in either direction. This suggests that BMI and process-oriented FMS, encompassing locomotor skill and object control skill, develop independently, possibly influenced by unexplored variables. These findings contradict earlier results based on product-oriented measurements, which may include a physical capacity component. The outcomes further underscore the importance of monitoring weight status from early childhood, given its significant association with later-life weight conditions.