We evaluated the efficacy and safety outcomes of endoscopic intradetrusor botulinum toxin A (BTA) injections for the treatment of children with neuropathic bladder (NB) and non-neuropathic bladder (NNB) with or without detrusor overactivity in a single centre with a retrospective analysis. For the period 2006–2015, children who received BTA in our hospital were analysed. They were divided into group 1, those with underlying NB and group 2, those without a clear neuropathic cause of symptoms (NNB). Data are given as percentages or medians (interquartile range). Over the study period, 52 children (28 boys, 54%) received BTA, 28 in group 1 (54%; 17 (61%) boys) and 24 in group 2 (46%; 11 (46%) boys). Age at first injection was 11.8 (9.5–14.4) years. After initial injection, 40 (77%) reported symptomatic improvement, 17 (43%) becoming dry. There was no significant difference in response to initial injection between groups (p = 0.11). Duration of improvement after first injection was 7 (5.8–14) months. Twenty-five (48%) had further injections, of whom 3 (12%) were initial non-responders. Ongoing improvement was reported in 20 (80%), 11 (44%) of whom were dry. There was no significant difference in overall response to injections between groups (p = 0.11). Of the 11 non-responders, none (0/3) improved after subsequent injection and 3 (27%) subsequently underwent major urological surgery. Of the 40 who responded, 2 (5%) underwent major surgery. BTA injection produced symptomatic improvement in 77% of our study population, with no significant differences in response between NB and NNB groups. In 95% of those who improved, major urinary tract procedures were avoided during the period studied. None of the initial non-responders improved after subsequent BTA injection. BTA injection is effective and reliable in the management of children with NB and NNB refractory to medical therapy.