Abnormal functional brain networks could be involved in the development of temporal lobe epilepsy (TLE). In this longitudinal resting-state fMRI study, changes in functional networks during epileptogenesis in the intraperitoneal kainic acid (IPKA) rat model for TLE were mapped. Therefore, resting-state fMRI was acquired at several time points during epileptogenesis to identify functional networks that were analysed and compared with graph theory. Our results suggest that network connections in the functional brain network progressively become weaker during epileptogenesis. We also find a decreased segregation and integration of the network.