There remains limited understanding of population-level patterns of mental disorder prevalence for first- and second-generation immigrant and refugee children and youth and how such patterns may vary across mental disorders. To examine the diagnostic prevalence of conduct, attention-deficit/hyperactivity disorder (ADHD), and mood/anxiety disorders in immigrant, refugee, and nonimmigrant children and youth in British Columbia, Canada. This retrospective, population-level cohort study examined linked health administrative records of children and youth in British Columbia (birth to age 19 years) spanning 2 decades (1996-2016). Physician billings, hospitalizations, and drug dispensations were linked to immigration records to estimate time-in-British Columbia-adjusted prevalence of mental disorder diagnosis among children and youth from immigrant or refugee backgrounds compared with those from nonimmigrant backgrounds. Analyses were conducted from August 2020 to November 2021. The diagnostic prevalence of conduct, ADHD, and mood/anxiety disorders were the main outcomes. Results were stratified by migration category (immigrant, refugee, nonimmigrant), generation status (first- and second-generation), age, and sex. A total of 470 464 children and youth in British Columbia were included in the study (227 217 [48.3%] female). Nonimmigrant children and youth represented 65.5% of the total study population (307 902 individuals). Among those who migrated, 142 011 (87.8%) were first- or second-generation immigrants, and 19 686 (12.2%) were first- or second-generation refugees. Diagnostic prevalence of mental disorders varied by migration category, generation status, age, and sex. Children and youth from immigrant and refugee backgrounds (both first- and second-generation), compared with nonimmigrant youth, generally had a lower prevalence of conduct disorder (eg, age 6-12 years: first-generation immigrant, 2.72% [95% CI, 2.56%-2.90%] vs nonimmigrant, 7.03% [95% CI, 6.93%-7.13%]), ADHD (eg, age 6-12 years: first-generation immigrant, 4.30% [95% CI, 4.10%-4.51%] vs nonimmigrant, 9.20% [95% CI, 9.08%-9.31%]), and mood/anxiety disorders (eg, age 13-19 years: first-generation immigrant, 11.07% [95% CI, 10.80%-11.36%] vs nonimmigrant, 24.54% [95% CI, 24.34%-24.76%]). Among immigrant children and youth, second-generation children and youth generally showed higher prevalence of conduct, ADHD, and mood/anxiety disorders than first-generation children and youth (eg, ADHD among second-generation immigrants aged 6-12 years, 5.94% [95% CI, 5.75%-6.14%]; among first-generation immigrants aged 6-12 years, 4.30% [95% CI, 4.10%-4.51%]). Second-generation refugee children had the highest diagnostic prevalence estimates for mood/anxiety in the 3-to-5-year age range relative to first- and second-generation immigrant and nonimmigrant children (eg, second-generation refugee, 2.58% [95% CI, 2.27%-2.94%] vs second-generation immigrant, 1.78% [95% CI, 1.67%-1.89%]). Mental disorder diagnoses also varied by age and sex within immigrant, refugee, and nonimmigrant groups. These findings show differences in diagnostic mental disorder prevalence among first- and second-generation immigrant and refugee children and youth relative to nonimmigrant children and youth. Further investigation is required into how cultural differences and barriers in accessing health services may be contributing to these differences.