Introduction There is evidence of an increased risk of motor neuron disease (MND) in military that is mainly based on studies performed in the US. We used health insurance databases to conduct a French nationwide case-control study in order to study the association between being military and MND. Methods We identified incident MND cases between 2010 and 2015 in France using a previously developed algorithm that is based on drug claims (Riluzole), hospitalization records (ICD-10 code G122), and benefits for long-term chronic diseases. Each case was randomly matched on age, sex, and residency area (departement) to 10 controls selected among all persons who were reimbursed any health care during the year of incidence of the matched case. We defined military personnel as persons affiliated to the “Caisse Nationale Militaire de Securite Sociale” (CNMSS) or the general scheme of the social security with a military status. We examined the association between military and MND using conditional logistic regression in order to compute odds ratios (ORs) and 95% confidence intervals (95% CI). All analyses were performed separately in men and women. We also performed analyses restricted to retired military (specific code for retired CNMSS affiliates). Results Of all the MND cases identified in France during the study period (n = 13,082), 12,729 (97%) had correct data for the matching variables and information on type of social security; they were matched to 127,283 controls. Among cases, mean age at incidence year was 67 years in men and 70 years in women, and 55% were men. The proportion of military was of 1.8% and 1.6% among male cases and controls, and of 0.7% and 0.8% among female cases and controls. There was no association between military and MND in women (OR = 0.89; 95% CI: 0.65–1.23). In men, there was a trend towards a small increased risk of MND both for military overall (OR = 1.13; 95% CI: 0.94–1.36) and retired military (OR = 1.16; 95% CI: 0.95–1.43) that was not statistically significant. Conclusion This French nationwide study did not show a statistically increased risk of MND among military personnel between 2010 and 2015, although there was a trend towards a small increased risk in men. The broad definition of military in our study that includes workers with different occupations and professional exposures is a limitation of our study. We plan to pursue these analyses by adjusting for additional covariates and extending the study period.