The Global School-based Student Health Survey (GSHS) collects data from early adolescents who are approximately 13–15 years old and enrolled in middle schools (also known as junior secondary schools). We used logistic regression models to examine the associations between self-reported hygiene practices and mental health status as assessed by the 2007 India GSHS. Then, we used meta-analysis to compare the results from India with those from 11 other GSHS-participating countries in Asia and Africa (Djibouti, Indonesia, Jordan, Kenya, Lebanon, Myanmar, the Philippines, Tanzania, Thailand, Uganda, and the United Arab Emirates). Among 7904 middle school students in India, 25.5% reported symptoms of depression, 8.6% reported loneliness, and 7.8% reported anxiety-related insomnia. Both males and females who reported symptoms of depression had an increased likelihood of poor hand and oral hygiene, including washing their hands rarely or never and brushing their teeth less than daily. The meta-analysis for this association yielded statistically significant pooled odds ratios for both boys and girls. In girls, loneliness was also associated with poor hand and oral hygiene. Reduced mental health status in adolescents may lead to worse hygiene behaviors and an increased risk of infections. Teachers, parents, healthcare workers, and other adults who observe suboptimal hygiene status in an adolescent should consider whether this indicates a mental health issue that requires clinical services.