Background: To assess the effect of individualized oral health care training (IndOHCT) administered to 6–16-year-old psychiatric in-patients on dental plaque removal. Methods: 74 in-patients with mental health disorders (49 males) aged 6–16 years with a mean age of 10.4 ± 2.3 years, were randomly divided into two equal groups. At the start of hospitalization, one calibrated dentist assessed the oral health status in the hospital setting. In-patients of the intervention group (IG) received IndOHCT, while those of the control group (CG) got an information flyer. Dental plaque was assessed by the Turesky modified Quigley-Hein-Index (TI) at the start (t0) and at the end of hospitalization before (t1a) and after (t1b) autonomous tooth brushing. Results: During hospitalisation, the TI was reduced in both groups (t0→t1a: IG = −0.1; CG = −0.2, p = 0.71). However, in-patients receiving IndOHCT achieved significantly higher plaque reduction rates than the controls when plaque values before and after autonomous tooth brushing were compared (t1a→t1b: IG = −1.0; CG = −0.8; p = 0.02). The effect size (ES) demonstrates the efficacy of IndOHCT (ES = 0.53), especially in children with mixed dentition (ES = 0.89). Conclusions: IndOHCT enabled hospitalized children and adolescents with mental health disorders to achieve a better plaque reduction by tooth brushing but failed to improve self-controlled routine oral hygiene.