Background The prevalence of anemia in female adolescents increases every year. A duodenal Cytochrome B ( CYBRD1) enzyme is involved in the regulation of iron metabolism. G797A gene polymorphism of the CYBRD1 reduces nonheme iron transport into the enterocytes, which was mediated by the divalent metal transporter 1 protein. Daily consumption of fruits and vegetables has been recommended for the prevention of non- communicable diseases, including anemia. Aim This study aimed to analyze the association of CYBRD1 polymorphism and daily consumption of fruits and vegetables with anemia in female adolescents in the Karanganyar regency. Methods This cross-sectional study recruited 233 female students in 6 senior and vocational high schools in Karanganyar regency, which were selected using purposive sampling. Data on fruit and vegetable consumption were collected using Semi-Quantitative Food Frequency Questionnaire (SQ-FFQ). Polymorphism of the G797A CYBRD1 gene was determined using the amplification refractory mutation system polymerase chain reaction. All collected data were analyzed using chi-square and multiple logistic regression tests with p < 0.05. Results Anemia was found in 13.73% of female students. Inadequate intakes of fruits and vegetables were found in 63.09 and 51.07% of female students, respectively. The AA genotype (OR = 5.779; 95%CI: 0.974–34.289; p = 0.053), inadequate fruit consumption (OR = 1.497; 95%CI: 0.603–3.718; p = 0.133), and inadequate vegetable consumption (OR = 11.99; 95%CI: 3.457–41.586; p < 0.001) increased higher risk of anemia, compared with their counterparts. Conclusions G797A CYBRD1 gene polymorphism and daily consumption of vegetables increase the risk of anemia but not for daily consumption of fruits in female adolescents in the Karanganyar regency.