Background Research has revealed a possible connection between dietary folate intake and the risk of spontaneous abortion (SA). Interestingly, the FTO gene may play a dual role, influencing both folate needs and SA susceptibility. Therefore, this research sought to investigate the interaction between FTO genotypes, dietary folate intake, and the potential risk of SA. Methods This case-control study was conducted on 539 adult women, including 192 women with a history of SA and 347 women without a history of abortion. To evaluate FTO gene genotypes for the presence of rs9939609 polymorphism, 5 ml of blood was collected from all participants. A validated semi-quantitative food frequency questionnaire (FFQ) was used to assess the dietary folate intake. Binomial logistic regression was used to investigate the relationship between folate intake and SA in carriers of different FTO genotypes. Results A negative association was found between dietary folate intake and SA, especially in females with the AA genotype of FTO rs9939609 polymorphism (OR=0.97, 95% CI 0.95–0.99, P=0.04). The statistical significance of this link persisted even after adjusting for age, body mass index (BMI), drinking alcohol, smoking, and dietary intake. Conclusions This study indicates that dietary folate intake may protect against SA, particularly in women who have the FTO rs9939609 polymorphism. However, more investigation is required to confirm these findings and elucidate the underlying mechanisms linking SA, the FTO gene, and folate intake