This study aims to investigate the relationship between motor skills at age 7 and spinal pain at age 11. The study included participants from the Danish National Birth Cohort. Data on motor skills were obtained from the Developmental Coordination Disorder Questionnaire, completed by the mothers when the children were 7 years old, and spinal pain was self-reported at age 11 for frequency and intensity of neck, mid back, and low back pain. This was categorized into “no,” “moderate,” or “severe” pain, based on frequency and pain intensity. Associations were estimated using multinomial logistic regression models. Data on both motor skills and spinal pain was available for 25,000 children. There was a consistent pattern of reporting more neck or mid back pain at age 11 for those with lower levels of fine motor skills and coordination scores at age 11. The relationship was significant for severe pain (the highest relative risk ratio being 1.87 and the lowest 1.18), but not for moderate pain (the highest relative risk ratio being 1.22 and the lowest 1.07). Gross motor skills were not associated with spinal pain, and there was no relationship between low back pain and motor skills.Conclusion: Our results indicate a link between motor development at 7 years of age and neck and mid back pain, but not low back pain, at 11 years of age. Improvement of motor skills in young children might reduce the future burden of neck and mid back pain and should be a target of future research.What is Known:•Spinal pain in preadolescence and adolescence is common and 
predisposes to spinal pain in adulthood.•Motor skills influence the biomechanics of movement and therefore has a 
potential impact on musculoskeletal health.What is New:•Poor fine motor- and coordination skills in childhood were associated with increased risk of severe neck- or mid back pain, but not low back pain, four 4 years later.•Poor gross motor skills were not associated with higher risk of later spinal pain.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00431-023-04964-8.