Scotland benefits from an integrated national healthcare team for motor neurone disease (MND) and a tradition of rich clinical data capture using the Scottish MND Register (launched in 1989; one of the first national registers). The Scottish register was re-launched in 2015 as Clinical Audit Research and Evaluation of MND (CARE-MND), an electronic platform for prospective, population-based research. We aimed to determine if incidence of MND is changing over time. Capture–recapture methods determined the incidence of MND in 2015–2016. Incidence rates for 2015–2016 and 1989–1998 were direct age and sex standardised to allow time-period comparison. Phenotypic characteristics and socioeconomic status of the cohort are described. Coverage of the CARE-MND platform was 99%. Crude incidence in the 2015–2017 period was 3.83/100,000 person-years (95% CI 3.53–4.14). Direct age-standardised incidence in 2015 was 3.42/100,000 (95% CI 2.99–3.91); in 2016, it was 2.89/100,000 (95% CI 2.50–3.34). The 1989–1998 direct standardised annual incidence estimate was 2.32/100,000 (95% CI 2.26–2.37). 2015–2016 standardised incidence was 66.9% higher than Northern European estimates. Socioeconomic status was not associated with MND. Our data show a changing landscape of MND in Scotland, with a rise in incidence by 36.0% over a 25-year period. This is likely attributable to ascertainment in the context of improved neurological services in Scotland. Our data suggest that CARE-MND is a reliable national resource and findings can be extrapolated to the other Northern European populations.