Recently, an increase in the incidence of inflammatory bowel disease (IBD) has been observed, especially among children and adolescents. Currently, few studies focus on the differentiation of inflammation in IBD subunits, i.e., Crohn’s Disease (CD) and Ulcerative Colitis (UC). The aim of this study was to compare the concentrations of proinflammatory mediators of arachidonic acid (ARA) and linoleic acid (LA) in patients with CD (n = 34) and UC (n = 30), in order to identify differences in inflammation in both diseases and within the same entity, according to disease activity. Sixty-four adolescents with a mean age of 13.76 ± 2.69 and 14.15 ± 3.31, for CD and UC, respectively, were enrolled in the study. Biochemical analysis of ARA and LA derivatives was performed using a liquid chromatography. A trend was observed in the concentration of 15S-HETE (hydroxyeicosatetraenoic acids) in CD relative to UC. The active phase of both diseases showed a higher 15S-HETE concentration in active CD relative to active UC. Comparing patients with CD with active and inactive disease showed a trend of increased levels of thromboxane B2, leukotriene B4 and 9S-HODE (hydroxyoctadecadienoic acid) in the active versus the inactive disease. We also observed statistically significantly higher levels of 12S-HETE in inactive CD relative to active CD. In the UC group, on the other hand, statistically significantly higher levels of prostaglandin E2 and 16RS-HETE were observed in active UC relative to inactive UC. Moreover, significantly higher concentrations of LTX A4 5S, 6R were observed in inactive UC relative to the active phase. In conclusion, the present study indicated the activity of the 15-LOX pathway in CD. Further studies involving lipid mediators in patients with IBD may contribute to the development of new therapies for the treatment of IBD. The identification of differences in the course of inflammation may help to target therapy in CD and UC, and perhaps allow the introduction of an additional diagnostic marker between the two main IBD subtypes.