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Introduction Neurogenic bowel dysfunction (NBD) is common in multiple sclerosis (MS), frequently presenting with constipation and faecal incontinence and impairing quality of life. NBD may also impact neurogenic bladder function. Transanal irrigation (TAI) is increasingly used to manage NBD, but comparative evidence in MS is limited.Methods This prospective, multicentre, randomised controlled superiority trial compared TAI using Navina Smart with SBC. Adults with MS and confirmed NBD were randomised 1:1. The primary endpoint was change in constipation and/or faecal incontinence severity using the Cleveland Clinic Constipation Score and Wexner score at 8 weeks. Secondary outcomes included changes at 4 and 8 weeks, NBD score, bowel-related quality of life, bladder-specific quality of life (SF-Qualiveen), adherence and safety. Analyses were performed using non-parametric tests.Results Eighty-six patients were randomised; 84 comprised the intention-to-treat cohort and 76 the per-protocol cohort. Baseline constipation and NBD severity were greater in the TAI arm. At 8 weeks, constipation improved more with TAI than SBC (mean Cleveland score change −5.11 ± 4.96 vs −1.56 ± 3.52; p = 0.0002), while faecal incontinence did not reach superiority at this time point (Wexner −3.34 ± 4.38 vs −1.18 ± 4.47; p = 0.073). At 4 weeks, TAI improved both constipation (−6.03 ± 4.61; between-group p = 0.0001) and faecal incontinence (−5.17 ± 4.28; p = 0.0011), whereas SBC improved constipation only (−1.95 ± 3.75; p = 0.0026). NBD severity improved significantly with TAI at both 4 and 8 weeks (both p < 0.0001), with no significant improvement in the SBC group (p = 0.0545 at 4 weeks; p = 0.5384 at 8 weeks); between-group differences favoured TAI at both time points (both p < 0.0001). Bowel-related quality of life improved significantly within the TAI group at 8 weeks, with no significant change in the SBC group and no significant between-group difference. Bladder-related quality of life improved significantly within the TAI group (SF-Qualiveen Overall score change −0.35 ± 0.64; p = 0.0024) but not with SBC (−0.23 ± 0.76; p = 0.0825), with no significant difference in change between groups (p = 0.5544). Adherence was high (97% TAI; 100% SBC). No serious adverse events occurred in the per-protocol safety population.Conclusion Transanal irrigation with Navina Smart improves constipation and overall bowel dysfunction in MS-related NBD, with early benefits in faecal incontinence and sustained improvement in NBD severity. In addition to bowel symptom control, TAI produces a modest but significant within-group improvement in bowel-related and bladder-related quality of life. High adherence and a favourable safety profile support TAI as an effective therapeutic option for managing NBD in MS.