The direction of the longitudinal relationship between physical activity (PA) and fundamental motor skills (FMS) remains unclear. We evaluated the bi-directional, prospective relationships between intensity-specific physical activity (PA) and domain-specific fundamental motor skills (FMS) over 2 years in children attending preschool at baseline. A sample of 230 children (mean age at baseline 4.7 yr, 52% boys) from the 'Sogn og Fjordane Preschool Physical Activity Study' was measured 2 years apart. PA was assessed using ActiGraph accelerometers (GT3X+). FMS were evaluated by a test battery guided by the 'Test of Gross Motor Development 3' and the 'Preschooler Gross Motor Quality Scale'. PA outcomes were total PA (TPA [counts per minute]) and intensity specific PA and sedentary behaviour (SED) (min/day). FMS outcomes were locomotor, object control, and balance skills. Linear mixed model adjusting for potential co-variates was used to evaluate the bi-directional prospective associations between these variables, including the moderating effect of sex and age. Baseline total PA, moderate-to-vigorous PA (MVPA), and vigorous PA predicted higher locomotor, object control, and balance skills at follow-up (standardized regression coefficient (β): 0.17 to 0.26, p = 0.002-0.017). Baseline SED predicted lower locomotor skills at follow-up (β: - 0.27, p = 0.012). Baseline light PA did not predict FMS at follow-up. Baseline FMS were not associated with PA or SED at follow-up. MVPA was positively associated with development of FMS in young children. In contrast, FMS were not related to future PA levels. Our results suggest promotion of MVPA is important for FMS development in young children.