Inflammatory Bowel Disease (IBD) is a group of chronic intestinal diseases, among which Crohn’s disease (CD) and ulcerative colitis (UC) represent the two main types. The differential diagnosis of these two disorders is often a significant challenge, as there is a lack of specific and non-invasive biomarkers. In this study, we assessed the serum profile of proinflammatory mediators (E- and P-selectin, CCL2, IL-1α, IL-12p70, TNF-α) in patients with IBD to identify biomarkers helpful in the differential diagnosis of CD and UC. The conducted statistical analyses revealed a significant increase in E-selectin, P-selectin, IL-1α, and IL-12p70 levels in the serum of CD patients compared to UC. The performed ROC curve analysis identified moderate values of E-selectin (AUC 0.752), P-selectin (AUC 0.733), and IL-1α (AUC 0.731) in differentiating CD from UC, while IL-12p70 presented a satisfactory value (AUC 0.695). Simultaneous measurements of each biomarker with serum calprotectin improved the ability of E-selectin (AUC 0.752 vs. 0.829), P-selectin (AUC 0.733 vs. 0.75), IL-1α (AUC 0.731 vs. 0.778), and IL-12p70 (AUC 0.695 vs. 0.714) to differentiate CD from UC. Moreover, we identified a significant relationship between the concentration of CCL2 (r = 0.566, p < 0.005) and TNF-α (r = 0.431, p < 0.05) and the disease activity expressed as the Mayo score in the UC group. We also identified a significant relationship between the concentration of E-selectin (r = 0.372, p < 0.05), CCL-2 (r = 0.55, p < 0.05), IL-1α (r = 0.637, p < 0.005), and TNF-α in the group of patients with UC. Another significant correlation in the UC group was noted in the case of E-selectin and IL-12p70 (r = 0.542, p < 0.05), as well as between IL1-α and P-selectin (r = 0.514, p < 0.05). The results obtained in this study indicate the potential use of E-selectin, P-selectin, IL-1α, and IL-12p70 serum profiles in differentiating CD from UC. Regarding the significant relationship of CCL2 and TNF-α with the Mayo score, these two biomarkers might be useful in assessing and monitoring the disease activity during UC.