The two-compartment intravoxel incoherent motion (IVIM) theory assumes that the transverse relaxation time is the same in both compartments. However, blood and tissue have different T2 values, and echo time (TE) may thus have an effect on the quantitative parameters of IVIM. The purpose of this study was to investigate the effects of TE on IVIM-DWI-derived parameters of the prostate. In total, 17 healthy volunteers underwent two repeat examinations. IVIM-DWI data were scanned 6 times with variable TE values of 60, 70, 80, 90, 100, and 120 ms. The ADC of a mono-exponential model and the D, D*, and f parameters of the IVIM model were calculated separately for each TE. Repeat measures were assessed by calculating the coefficient of variation and Bland-Altman limits of agreement for each parameter. Spearman’s rho test was used to analyse relationships between IVIM indices and TE. Our results showed that TE had an effect on IVIM quantification, which should be kept constant in the examination protocol at each individual institution. Alternatively, an extended IVIM could be used to eliminate the effect of the TE value on the quantitative parameters of IVIM. This may be helpful for guiding clinical research, especially for longitudinal studies.