Recurrent aphthous stomatitis (RAS) is a benign ulcerative condition, defined by the recurrent formation of non-contagious mucosal ulcers. Surfactant protein D (SP-D) is secreted frequently at surfaces exposed directly to body fluids. This study aims to investigate the association of SP-D single nucleotide polymorphisms (SNPs) with the onset of RAS. Blood samples from 212 subjects (106 cases/controls each) were collected during 2019 and genotyped for SP-D SNPs (rs721917, rs2243639, rs3088308) by polymerase chain reaction and restriction fragment length polymorphism followed by 12% polyacrylamide gel electrophoresis. Minor aphthous (75.5%) was the commonly observed ulcer type as compared to herpetiform (21.7%) and major aphthous ulcers (2.8%). A family history of RAS was reported in 70% of cases. RAS was found significantly associated with rs3088308 genotypes T/A (95% (Cl): 1.57–5.03,p= 0.0005), A/A (95% (Cl): 1.8–6.7,p= 0.0002), T-allele (95% (Cl): 1.09–2.36,p= 0.01), A-allele (95% (Cl): 1.42–3.91,p= 0.01), rs721917 genotype T/T (95% (Cl): 1.15–25.35,p= 0.03), and T-allele (95% (Cl): 1.28–3.10,p= 0.002). Female gender and obese body mass index (BMI) were significantly associated with rs3088308 genotypes T/A (95% (CI): 1.89–15.7,p= 0.001), T/T (95% (Cl): 1.52–11.9,p= 0.005), A-allele (95% (Cl): 1.65–7.58,p< 0.001), and T-allele (95% (Cl): 1.4–10.1,p<0.001) and rs721917 genotype T/T (95% (CI) = 1.3–33,p= 0.02), respectively. This study describes the association of SP-D SNPs (rs721917, rs3088308) with RAS in the Pakistani population.