Background Undernutrition and the Human Immunodeficiency Virus (HIV) are related in a complex and harmful way and are both exceedingly prevalent throughout the world, particularly in sub-Saharan Africa. In Ethiopia, the prevalence of undernutrition ranged from 12.3–43% and the prevalence of stunting and thinness among HIV-infected adolescents were 39%) and 14% respectively. There is no study among young patients living with Human Immunodeficiency Virus and ART. Therefore, this study aims to assess the prevalence of undernutrition and its associated factor among young infected with HIV and following ART clinics at the north Shoa health facilities in Oromia, Ethiopia. Methods A facility-based cross-sectional study was conducted. A probability-proportional sampling method was used to select 387 participants and pretested, interview-administered questionnaires were used to collect the data. The information was entered into EpiData and analyzed with SPSS. A 95% confidence interval and a P-value less than 0.05 were used to identify predictor variables, and an adjusted odds ratio (AOR) was used to assess the strength of the association. Result The prevalence of stunting and thinness in the study was 37% (95% CI: 32.0,41.9) and 13.4% (95%, CI:10.3, 16.9) respectively. Being male (AOR 1.5, 95%CI: 1.0,2.4), educational level of caregiver(AOR 7.8, 95%CI: 3.5, 17.2), and having a family income ≤ 1500 ETB (AOR 7.8,95%CI:3.5,17.2) were significantly associated with stunting while being male (AOR = 2.59,95% CI: 1.25,5.40), nutritional counseling (AOR 4.05,95% CI:1.64,10.02), Skipping meal (AOR 4.97,95%CI:2.08,11.9) and educational level of caregiver (AOR 4.18,95% CI:1.82,9.60) were significantly associated with thinness. Conclusion The prevalence of stunting and thinness among HIV-infected adolescents and youth in the study area was consistent with EDHS and higher than the EDHS report respectively. Sex, skipping a meal, nutritional counseling, and family size were significantly associated with thinness and Sex, educational level of the caregiver, and family income was significantly associated with stunting.
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