Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS). However, only few studies have considered the association of high‐resolution HLA type and MS with none yet from Saudi Arabia. The aim of this study was to investigate the association of HLA class II alleles with MS in the Saudi population. We used next‐generation sequencing to investigate HLA association with MS. This study was conducted at King Abdulaziz Medical City in Riyadh, Saudi Arabia. We found that several HLA‐DRB1 and DQB1 alleles were associated with MS. These alleles included HLA‐DRB1*15:01 (odds ratio [OR]: 3.01; 95%, confidence interval [CI]: 1.68‐5.54; P = .0001), HLA‐DQB1*02:01 (OR: 1.76; 95% CI: 1.20‐2.58; P = .0022), HLA‐DQB1*06:02 (OR: 3.52; 95% CI: 1.87‐6.86; P < .0001), and HLA‐DQB1*06:03 (OR: 2.42; 95% CI: 1.16‐5.25; P = 0.01). Interestingly, HLA‐DRB1*15:01 was associated with increased risk of previous relapses. In addition, HLA‐DRB1*15:01 and HLA‐DQB1*06:02 were found to be associated with lower vitamin D levels. This study provides insights on the association of different HLA alleles with clinical characteristics and outcome of MS among Saudis. These insights can have future implications for the clinical management of MS based on the patient genetic profile.