The purpose of this study was to compare the functional status of children with acquired and congenital lower limb loss after 3 weeks and 6 months of prosthetic rehabilitation. Forty-one children aged between 8 and 17 years participated in the study. The children underwent prosthetic fitting, prosthetic training and rehabilitation after physiotherapy evaluations. Gait patterns and weight bearing values were assessed, and the Amputee Mobility Predictor (AMP) Questionnaire was applied. The congenital group had better gait patterns, weight bearing values and AMP scores in the initial assessment and after 3 weeks. The statistical analyses of the same parameters after 6 months showed that there were no significant differences between the two groups (P>0.05). It was determined that all congenital patients and only 16 of 20 acquired patients were wearing their prostheses for more than 8 h a day. When the outcomes of the first assessments were compared, the congenital group showed a better functional level, gait pattern and weight bearing value. At the end of 6 months, an improvement was observed in the functional level, gait pattern and weight bearing value in both the groups. The functional state, gait pattern and weight bearing value of children with limb loss can be improved if they actively use their prosthesis.