In adolescents, anaemia has been linked to affecting physical disorders, growth, and mental retardation and also increases reproductive morbidities among adolescent girls during their womanhood. It is believed that with increasing age, females are more prone to anaemia than their male counterparts. Unfortunately, the anaemia intervention program, such as the National Nutrition Anaemia Prophylaxis Programme, primarily targets infants, young children, pregnant and lactation women, and not adolescents. Therefore, this study tries to fill this gap and study the prevalence of anaemia and the associated factors among adolescent boys and girls residing in Uttar Pradesh and Bihar, India. Secondary data analysis was performed on cross-sectional survey data from the Understanding the Lives of Adolescents and Young Adults survey. The sample size was 20,594 adolescents aged 10–19 years in Uttar Pradesh and Bihar, India. The outcome variable was anaemia, and the explanatory variables were age, education, working status, media exposure, marital status, received IFA and deworming tablets, BMI status, stunting status, wealth index, caste, religion, residence, and States. Descriptive statistics and bivariate analysis were used to find the preliminary results. Multinomial regression analysis was carried out to provide the adjusted estimates. Overall, anaemia was more prevalent among adolescent girls than adolescent boys (20% vs. 8.7%). Moderate/severe anaemia was 0.24 and 0.49 times less likely among adolescent boys and girls, respectively, who had 10 and above years of schooling than adolescents with no schooling (p < 0.01). Rural adolescent boys were 1.49 times (p < 0.05) more likely to suffer from moderate/severe anaemia than urban counterparts. The odds for moderate/severe anaemia among adolescent boys were relatively higher among late adolescents, with no mass-media exposure, stunted, and rural adolescents. Similarly, odds for moderate/severe anaemia among adolescent girls were higher among late adolescents and adolescents without schooling and mass-media exposure. Prevalence of anaemia was higher among adolescent girls than in boys. Lower education status, rural residence, late adolescence, no exposure to mass media, and stunting were the predictors of moderate/severe anaemia among adolescents. Anaemia among adolescents must be addressed through effective public health policy targeting adolescents residing in rural areas. There is a need to disseminate information about anaemia-related programs, such as National Iron Plus Initiative (NIPI), through mass media, and subsequently, the public health system may be prepared to tailor the needs of adolescent boys and girls.