BACKGROUND: Japan is estimated to host 3000 cases of Chagas disease (CD). However, there are no epidemiological data and policies for prevention and care. We aimed to analyze the current situation of CD in Japan and identify possible barriers to seeking care. METHODS: This cross-sectional study included Latin American (LA) migrants living in Japan from March 2019 to October 2020. We obtained blood samples to identify participants infected with Trypanosoma cruzi, and data about sociodemographic information, CD risk factors, and barriers to access to the Japanese national health care system (JNHS). We used the observed prevalence to calculate the cost-effectiveness analysis of the screening of CD in the JNHS. FINDINGS: The study included 428 participants, most of them were from Brazil, Bolivia and Peru. The observed prevalence was 1.6% (expected prevalence= 0.75%) and 5.3% among Bolivians. Factors associated with seropositivity were being born in Bolivia, having previously taken a CD test, witnessing the triatome bug at home, and having a relative with CD. The screening model was more cost-effective than the non-screening model from a health care perspective (ICER=200,320 JPY). Factors associated with access to JNHS were being female, length of stay in Japan, Japanese communication skills, source of information, and satisfaction about the JNHS. INTERPRETATION: Screening of asymptomatic adults at risk of CD may be a cost-effective strategy in Japan. However, its implementation should consider the barriers that affect LA migrants in access to the JNHS. FUNDING: Nagasaki University and Infectious Diseases Japanese Association.