Objectives: Aerobic fitness and fundamental motor skills have both been related to children's academic achievement. Results of studies that have simultaneously related aerobic fitness and fundamental motor skills to academic achievement have provided inconsistent results, and the exact relations with achievement in distinct academic domains remain unknown. The current study examined unique relations between aerobic fitness, fundamental motor skills, and achievement in reading, mathematics and spelling. Method: In total, 891 students (mean age = 9.17 years, SD = 0.66) from 22 primary schools participated. Two multilevel structural equation models were constructed, with relations between aerobic fitness (20m-shuttle run test), fundamental motor skills (tested with items of the Körperkoordinationstest für Kinder and Bruininks-Oseretsky Test for Motor Proficiency) and: (1) overall academic achievement, or; (2) achievement in the domains of reading, mathematics, and spelling (assessed with standardized academic achievement tests). Results: Fundamental motor skills were more strongly related to overall academic achievement than aerobic fitness, but the exact relations differed by academic domain. Aerobic fitness predicted spelling achievement, whereas motor skills predicted reading achievement, and both were predictive of mathematics achievement. Conclusions: Although more research is needed to disentangle the exact way in which aerobic fitness, motor skills, and academic achievement are linked, the results suggest that children's academic achievement benefits most from engagement in various physical activities which target both aerobic fitness and gross motor skills. These findings emphasize the importance of providing children with opportunities to engage in a wide variety of sports and activities.