Failure to understand and address the problem of malnutrition and its associated factors among female adolescents could lead to a vicious cycle of intergenerational malnutrition. A cross-sectional study was conducted in six secondary schools of four rural municipalities in Darchula District, Nepal. Data collection for the study was conducted from November 2021 to February 2022. Four hundred female adolescent students aged 15 to 19 years old were selected using quota sampling. The study aims to examine the prevalence of malnutrition by assessing different levels of body mass index (BMI) that is thinness (BMI less than 18.5 kg/m2), normal (18.5 kg/m2 to 24.9 kg/m2), overweight (25 kg/m2 to 29.9 kg/m2) and obese (BMI more than or equal to 30 kg/m2). Along with BMI, factors associated with undernutrition, here identified as thinness, are assessed using a structured questionnaire. Additionally, key informant interviews and review of interventions was performed to understand the gaps in nutrition-related policies and programs of school going adolescents in the study district. Quantitative data analysis included a prevalence study and chi-square test along with simple and multiple logistic regression to obtain crude and adjusted odds ratio at 95% confidence interval for the significant factors with p < 0.05 identified in the chi-square test. Thematic analysis and reviews were used for the synthesis of qualitative data. The results show a 24.7% prevalence of thinness in the study participants. Pre-mensuration status (OR = 5.015, CI = 1.257–20.011, p < 0.022), father having a monthly paying job (OR = 4.384, CI = 1.135–16.928, p < 0.032), father’s foreign employment (OR = 6.96, CI = 1.649–29.377, p < 0.008), household (HH) food insecurity status (OR = 2.079, CI = 1.182–3.658, p < 0.011) and grain/roots/tuber as most commonly bought food (OR = 9.487, CI = 1.182–76.138, p < 0.034) were found to be significantly associated with thinness. Information from the qualitative part identified gaps in existing interventions for an improved nutritional outcome among school going adolescent females. Further studies to understand the nutritional practices and its contributory factors in relation to thinness is encouraged. Stakeholders are urged to effectively address the shortcomings in existing interventions and adopt a more adolescent-centered approach to enhance the nutritional status of female adolescents.