The present study aimed to evaluate the effectiveness of customized handle toothbrush in dental plaque removal in children with Down syndrome in comparison to children with no special needs. A randomized clinical trial was performed on 48 children aged 6–9 years old. Participants were divided into two groups (n = 24, children with no special needs or with Down syndrome). Each group was divided into two subgroups (customized and conventional toothbrush). Plaque accumulation was evaluated using Turesky modification of the Quigley–Hein plaque index (TMQHPI) at four times (pre-brushing (T0), post-brushing at baseline (T1), 1 week (T2) and 3 weeks (T3)), and the modified gingival index (MGI) was used to evaluate the gingivitis at three times (T0, T2 and T3). Data were statistically analyzed. Plaque accumulation and gingivitis decreased significantly for all groups between T0 and T3 (p < 0.05). Both customized groups demonstrated significant lower plaque accumulation compared to conventional groups (p < 0.05) at T1, T2 and T3 and significant lower gingivitis at T3. Customizing the toothbrush handle improved child’s ability for plaque control, especially in children with Down syndrome.