Background Adolescent is the population whose age between 10–19 years old. They are undergoing rapid growth, development and are one of the nutritionally at-risk groups who should need attention. Adolescent undernutrition is a worldwide problem. Even if this stage brings the second window of opportunity to break the intergenerational cycle of undernutrition little is known specifically in the study area. This study was conducted to assess the prevalence of undernutrition and its associated factors among school adolescent girls in Abuna Gindeberet district, Central Ethiopia, 2021. Methods Institution-based cross-sectional quantitative study design was conducted in Abuna Gindeberet district among 10–19 years adolescent girls attending primary and secondary schools from January 1–30, 2021. A systematic random sampling technique was used to select 587 adolescent girls. Data were collected by using interviewer-administered structured and anthropometric measurements. Data were coded, then entered into the Epi-info version 7.2.2.6 and exported to SPSS version 25 and WHO Anthro plus for analysis. Logistic regression analysis was done to identify predictors of under nutrition. Level of statistical significance was declared at p-value < 0.05. Results The overall magnitude of stunting and thinness were 15.4% [95% CI (12–18)] and 14.2% [95% CI (11–17)] respectively. Number of meals per day [AOR = 3.62, 95% C.I (2.16, 6.05)], adolescent girls of lower grades [AOR = 2.08, 95% C.I (1.07, 4.04)] and who did not begin menstruation [AOR = 1.71, 95% C.I (1.06, 2.73)] were significantly associated with stunting. Adolescent girls engaged in vigorous intensity activities [AOR = 2.51, 95% C.I (1.14, 5.54)], poor dietary diversity score [AOR = 4.05, 95% C.I (1.43, 11.46)] and adolescent age [AOR = 3.77, 95% C.I (1.06, 13.37)] were significantly associated with thinness among adolescent girls. Conclusions Adolescent girl's undernutrition is a public health problem in the study area. The number of meals per day, adolescent girls of lower grades and who did not begin menstruation were significantly associated with stunting as well as adolescent girls engaged in vigorous-intensity activities; poor dietary diversity score and adolescent age were significantly associated with thinness among adolescent girls. Therefore, government and other stakeholders should focus on these identified factors to improve the nutritional status of adolescent girls.