This study aimed to explore the association between ring finger protein 41 (RNF41) c.-206 T > A variant and susceptibility to congenital heart disease (CHD) in the Chinese Mongolian population. The association between RNF41 gene c.-206 T > A polymorphism and CHD was examined in two independent case-control studies consisting of 219 CHD patients and 208 healthy controls. Genotype was determined by direct sequencing of PCR products. We found that the genotype frequencies of RNF41 c.-206 T > A differ significantly between the two groups (P < 0.05). The TT and TA genotypes in the CHD group were 80.67 and 19.33%, respectively. On the other hand, the frequencies of TT and TA in the control group were 94.44 and 5.56%, respectively. Furthermore, the allelic frequencies of CHD patients (T, 90.34%; A, 9.66%) were significantly different as compared with those of non-CHD controls (T, 97.22%; A, 2.78%; χ2 = 4.031, P = 0.041). Our study demonstrates that the RNF41 c.-206 T > A polymorphism may be a risk factor for congenital heart disease in the Chinese Mongolian population.