Setting: Seven intervention districts with intensified childhood tuberculosis (TB) case-finding strategies implemented by a non-governmental organisation and seven control districts under the National Tuberculosis Programme, Nepal. Objectives: To assess the differences in childhood TB case registrations and case registration rates per 100 000 population between two time periods (Year 1 = March 2012–March 2013 and Year 2 = March 2013–March 2014) in intervention and control districts. Design: Retrospective record review using routinely collected data. Results: Childhood TB cases increased from 271 to 360 between Years 1 and 2 in the intervention districts (case registration rate from 18.2 to 24.2/100 000) and from 97 to 113 in the control districts (13.4 to 15.6/100 000): the increases were significantly higher in the intervention districts compared with the control districts. The increases were also significantly higher in children aged 0–4 years and in those with smear-negative pulmonary TB and extra-pulmonary TB. Of the various case-finding strategies, household contact screening, private-public mix services and mobile health chest camps produced the highest yield of TB. Conclusion: A package of intensified case-finding strategies in children was associated with an increase in childhood TB case registrations in Nepal. Additional diagnostic approaches to increase case registrations also need to be considered.