Background Despite the rising prevalence of Inflammatory Bowel Disease (IBD), age and sex differences in its outcomes remain understudied. We investigated age and sex differences in IBD patients using a nationwide study in Iran, the Iranian Registry of Crohn’s and Colitis (IRCC). Methods The IRCC is a national registry that gathered information on adult IBD patients since 2017. The collected data included demographic information, medication history, disease activity, comorbidities, diagnosis age, prognosis, the extent of ulcerative colitis (UC), Crohn’s disease (CD) location, and extraintestinal manifestations. The statistical methods included the independent Student’s t-test, Chi-square test, and binary logistic regression, using R version 4.2.2. Results Among the 9,392 IBD patients, 7,496 (3,600 females) and 1,896 (808 females) had UC and CD, respectively. Sex difference showed higher odds of active disease in the past six months in male CD patients (OR 1.24 [95%CI 1.03, 1.49]) vs. females, but in male UC patients, the OR was 0.85 [0.78, 0.93]. Severe disease was less likely in CD patients aged 19–59 and >60 vs. <18. Similarly, UC patients <18 had lower odds of severe disease vs. those aged 19–59 and >60. Conclusions This study emphasizes the importance of understanding age and sex differences in IBD outcomes. These findings contribute to the ongoing global discussion on IBD management and facilitate the development of targeted interventions and personalized care.