This study examined occupational status and factors associated with sick leave and disability pension among adult long‐term survivors previously treated with allogeneic stem cell transplantation (allo‐SCT) during childhood. Moreover, occupational status was compared to that of a reference group. Data were collected with questionnaires and from medical records. The SCT group included 59 adults (18–45 years old: response rate 63%) treated with allo‐SCT in childhood with a median of 17 (range 3–28) years earlier. The reference group included 296 individuals randomly selected from the general population. The results show that 54% of the long‐term survivors were working part‐ or full‐time and that 19% were on sick leave or disability pension. A larger proportion of the SCT group was on sick leave or disability pension (19% vs. 6%: p < .001) than of the reference group. The logistic regression analysis revealed that being on sick leave or disability pension among long‐term survivors was associated with late effects related to the allo‐SCT (OR 12.28: 95% CI 1.3–111.6: p = .03). The results underscore that long‐term survivors’ engagement in paid work is influenced many years after treatment and highlights the need to include vocational assistance in the rehabilitation following allo‐SCT in childhood.