Background: We compared the efficiency of two MRI diffusion weighted imaging (DWI) techniques: DWI with SPIR (DWISPIR) and DWI with STIR (DWISTIR), to estimate their eligibility for quantitative assessment of Crohn’s disease activity in children and adults. Methods: In inflamed terminal ileum segments (n = 32 in adults, n = 46 in children), Magnetic Resonance Index of Activity (MaRIA) was calculated, ADC values of both DWI techniques were measured, and the corresponding Clermont scores calculated. ADC values of both DWI techniques were compared between both and within each patient group, assessing their mutual correlation. Correlations between MaRIA and the corresponding ADC values, and Clermont scores based on both DWI techniques were estimated. Results: No correlation between ADC of DWISPIR and DWISTIR was observed (rho = 0.27, p = 0.13 in adults, rho = 0.20, p = 0.17 in children). The correlation between MaRIA and Clermont scores was strong in both techniques—in SPIR, rho = 0.93; p < 0.0005 in adults, rho = 0.98, p < 0.0005 in children, and, in STIR, rho = 0.89; p < 0.0005 in adults, rho = 0.95, p < 0.0005 in children. The correlation between ADC and MaRIA was moderate negative for DWISTIR (rho = 0.93, p < 0.0005 in adults, rho = 0.95, p < 0.0005 in children), but, in DWISTIR, no correlation between ADC and MaRIA score was observed in adults (rho = −0.001, p = 0.99), whereas children presented low negative correlation (rho = −0.374, p = 0.01). Conclusions: DWISTIR is not suitable for quantitative assessment of Crohn’s disease activity both in children and adult patients.