Background: Kindergartens can potentially contribute substantially to the daily level of physical activity and development of motor skills and might be an ideal setting for improving these as a public health initiative. We aimed to examine whether children from rural outdoor kindergartens had a lower risk of motor difficulties than children from urban conventional kindergartens. Methods: Motor test results were measured during the first school year by school health nurses using a six-item test of gross- and fine motor skills (jumping, handle a writing tool, cutting with a scissor following a line, one-leg stand on each leg, throwing and grabbing). Register-based information was available on potential confounding factors. Results: We included 901 children from outdoor kindergartens and 993 from conventional kindergartens with a mean (SD) age of 6.5 years (0.4). The children from the two types of kindergarten differed according to demographic information, with outdoor kindergarten children more often being from more affluent families (long maternal education level: 47.5% vs. 31.0%, p < 0.0001) and fewer girls attending the outdoor kindergartens (42.7% vs. 49.5%, p = 0.003). In the adjusted models, we found no evidence of differences in the risk of motor difficulties between children attending either type of kindergarten (OR: 0.95, 95%CI: 0.71; 1.27, p = 0.72). Conclusion: Our results do not support outdoor kindergartens as a potential intervention to improve motor abilities among children. Randomized controlled trials are needed to confirm these findings.