Background: FUNDES-Child-SE is a proxy rating questionnaire for measuring participation and independence in children with disabilities in a Swedish context. It includes the components of frequency of attendance, engagement and independence. The original, Taiwanese FUNDES-Child 7.0, has previously been found to have a four-factor structure for frequency of participation and a two-factor structure for independence. The aim of this study was to test the factor structure in FUNDES-Child-SE. The factor structure is an important part of construct validity. Methods: Caregivers of 163 children with disabilities aged 6–18 years participated in this cross-sectional study. Exploratory factor analysis was used to find the factor structure for Engagement. Confirmatory factor analysis was used to test the factor structure for all three components. Results: The proposed factor structure for frequency of participation (daily living participation frequency, mobility participation frequency, learning participation frequency and community participation frequency) and independence (daily living independence and social participation independence) fit with data from FUNDES-Child-SE after excluding three to five items and adding two to five covariances of residuals. In the engagement component, two factors, named engagement in informal activities and engagement in formal activities, were found. After excluding one item and adding 10 covariances of residuals, the factor structure had an acceptable fit to data. Conclusions: Differences in components' factor structure indicate that attendance and engagement are separate aspects of participation. Before using numeric scores from FUNDES-Child-SE in clinical settings, responsiveness and interpretability should be evaluated.