Iron deficiency anemia (IDA) in adolescent girls is a problem that has not been resolved. This study aimed to explore the critical aspects of an integrated health care system model for preventing IDA in adolescent girls in a rural area of Indonesia. This qualitative research employed a grounded theory approach in order to build a substantive theory. This study used in-depth interviews with adolescents, parents, teachers, health workers, and persons in charge of adolescent programs at the health office, education office, and ministry of religion. Purposive sampling was performed until data saturation was achieved. Codes, categories, and themes were generated through thematic data analysis to develop a substantive theory. Data analysis was performed using MAXQDA 2022 software. A total of 41 people participated in this study. This investigation generated twenty-two categories and seven themes. These themes relate to policymaker commitments, stakeholder governance, quality, adolescents’ lifestyles, adolescents’ self-factors, adolescents’ access to health services, and social support. The themes identified become fundamental aspects of the integrated health care system model for preventing IDA in adolescent girls. The model of the integrated health care system consists of several essential points, which include awareness and efforts from policymakers and adolescent girls, supported by parents, teachers, and the community.