<b><i>Objectives:</i></b> This study aimed to evaluate whether vitamin D deficiency is associated with the severity of symptoms of irritable bowel syndrome (IBS) patients. Stress and gut inflammation can increase the serum level of corticotropin-releasing hormone (CRH) and interleukin-6 (IL-6), leading to a change in bowel movements. The aim of this study was to evaluate the anti-inflammatory and psychological effects of vitamin D3 supplementation on the symptom improvement of patients with a diarrhea-predominant form of IBS (IBS-D). <b><i>Methods:</i></b> Eighty-eight IBS-D patients (age: 18–65 years) based on Rome IV criteria who suffered from vitamin D deficiency and/or insufficiency were enrolled in this randomized, placebo-controlled trial from February 2017 to May 2018 at Rasoul-e-Akram Hospital, Tehran, Iran. Participants were randomly divided into two groups. The intervention group received 50,000 IU vitamin D3 weekly and the control group received a placebo for 9 weeks. All patients received Mebeverine 135 mg twice a day besides supplementation. The IBS Severity Score System (IBS-SSS), serum 25(OH) vitamin D3, CRH, and IL-6 were measured before and after interventions. <b><i>Results:</i></b> Seventy-four patients completed the study. The severity of IBS symptoms (<i>p</i> < 0.01) and IL-6 (<i>p</i> = 0.02) decreased significantly in the intervention group as compared to the control group, but there was no significant difference in the serum level of CRH. Also, in the treatment group, IBS-SSS and IL-6 were significantly reduced at the end of the study from baseline (<i>p</i> < 0.01 and <i>p</i> < 0.03, respectively). <b><i>Conclusion:</i></b> Our findings indicate that vitamin D3 supplementation can modulate the serum level of CRH and IL-6 and can improve symptoms in IBS-D patients. Vitamin D3 supplementation should be considered in IBS-D patients who suffer from vitamin D deficiency and/or insufficiency.