We investigate the evolution of the electron mobility of two different acceptors, [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) and indene-C60 bisadduct (ICBA), in a poly(3-hexylthiophene) blend solar cell during a prolonged thermal aging process. High electron mobility does not correlate with the best device performance in our study of the P3HT:PC71BM and P3HT:ICBA systems. Very little changes are observed in the polymer crystallinity as a function of time. The evolution of the acceptor appears to be the dominant factor that leads to long-term changes in the device performance. The electron mobility evolves differently in PC71BM and ICBA systems, which highlights the importance of the fullerene molecular structure.