fMRI-based retinotopic mapping was used to assess systematic variations in activated cortical surface area, amplitude, and coherence across sessions. Seven healthy subjects were scanned at 7 T in three separate sessions with intervals of 51.4 ± 5.4 days (Sessions 1 and 2) and 167.9 ± 24.4 days (Sessions 2 and 3). We found a reduction between Sessions 1 and 2 for activated cortical surface area, between Sessions 1 and 3 for amplitude, and between Sessions 1 and 2/3 for coherence. The results do not support head motion as a major cause of the observed effect seen in Session 1, suggesting that cognitive effects were the underlying cause of change. The phase correlations for both eccentricity and polar angle mapping were highly correlated between sessions, demonstrating the stability of the maps. Furthermore, the sensitivity in determining inter-session changes of cortical surface area, response amplitude, and coherence were, at a 5% significance level, estimated to be 1.5, 6, and 5%, respectively. Any future longitudinal fMRI study should carefully evaluate activation across sessions to determine the eligibility of inclusion of all time points. This experimental design provides guidance in methodological issues of clinical longitudinal fMRI-studies, specifically regarding effects of subject experience.