We investigated direct and indirect cross-sectional associations of physical activity, fundamental motor skills, executive functions, and early numeracy in preschoolers. The participants were 214 preschoolers aged three to five years. Time spent in moderate and vigorous physical activity was measured by hip-worn accelerometers and fundamental motor skills using the tasks assessing locomotor, object control, and stability skills. Inhibition/switching and working memory/updating, as components of executive functions, were assessed by computerized tests and a standardized test was used to assess early numeracy. Path analyses were used to examine direct and indirect associations between the constructs. Our results showed that stability skills were indirectly positively associated with early numeracy through inhibition/switching (β = 0.07, p < 0.05, 95 % CI [0.02, 0.14]) and locomotor skills through working memory/updating (β = 0.13, p = 0.001, 95 % CI [0.06, 0.20]). Vigorous physical activity was positively associated with early numeracy through locomotor skills and working memory/updating (β = 0.04, p = 0.01, 95 % CI [0.01, 0.07]) and negatively associated with early numeracy through inhibition/switching (β = -0.06, p < 0.05, 95 % CI [-0.11, -0.02]). Our findings indicate that by providing opportunities for vigorous physical activities and supporting motor skills learning, it may be possible to promote executive functions and early numeracy in preschoolers.