Purpose: This study aimed to investigate the relationship between fundamental movement skills (FMS) and markers of health among a cohort of Irish primary school children. Methods: Participants (N = 296, mean age: 7.99 ± 2.02 years) were senior infant (n = 149, mean age: 6.02 ± 0.39 years) and 4th class (n = 147, mean age: 9.97 ± 0.40 years) students from three primary schools in Cork, Ireland. FMS proficiency (TGMD-2) and markers of health (BMI percentile, waist circumference percentile, blood pressure percentiles, resting heart rate, cardiorespiratory fitness, objectively measured physical activity; PA) measurements were recorded. Correlation and hierarchical stepwise multiple linear regression analyses were conducted to investigate the relationship between FMS and markers of health. Results: A small, positive relationship was found between FMS (Gross Motor Quotient; GMQ) and cardiorespiratory fitness with small negative correlations between GMQ and 550 m time SDS among 6-year-olds (r(129) = -0.286, p < 0.05) and 10-year-olds (r(132) = -0.340, p < 0.05). A moderate, positive correlation was found between GMQ and light PA (r(71) = 0.400, p < 0.05). Small positive correlations were revealed between GMQ and moderate PA (r(71) = 0.259, p < 0.05) and between GMQ and total PA (r(71) = 0.355, p < 0.05). After adjusting for age, sex, the interaction effect of age and sex, and school attended, FMS explained 15.9% and 24.8% of the variance in 550 m time SDS among 6- and 10-year-olds, respectively, and 6% and 6.5% of the variance in light PA and moderate PA, respectively. After adjusting for age and sex, FMS explained 11.6% of the variance in total PA. Conclusion: A wide range of FMS is important for children's cardiorespiratory fitness and PA.