Background: Many patients who undergo emergency laparotomy are working, which is a key determinant for an individual’s socio-economic status and financial security. The objectives of this study were to compare labour market participation and sick leave in a nationwide patient population undergoing non-malignant emergency resections with a matched reference population. Methods: This nationwide prospective cohort study included all patients aged 18+ years undergoing emergency laparotomy for non-malignant disease resulting in intestinal resections, ostomy or drainage at Danish hospitals 2003–2014 and who were active on the labour market (n = 2895). We included a sex- and age-matched reference population (n = 11,422) and followed all persons in nationwide registers. We used survival analyses and logistic regression. Results: The proportion of people active in the labour market was 85% and 66% 1 and 2 years after surgery compared to 96% and 79% among the reference population. The hazard ratio of dropout was 1.15 (95% CI 1.05–1.25, p = 0.002) among patients compared to reference population. Increased dropout was observed for disability pension (2.58; 2.14–3.11; p < 0.0001), while patients did not have increased rate of age-related pensions. The proportion on sick leave was 66% the month following surgery compared to 3–4% among references. The proportion decreased thereafter but was higher up to 3 years after surgery. Conclusions: This nationwide study including all patients undergoing resections demonstrated marked increase in disability pensioning and sick leave after surgery compared to a matched reference group. This supports the need for interventions and programmes during hospital stay and after discharge focusing on labour market participation.