Purpose: This longitudinal study aimed to disentangle the impact of chemotherapy on fatigue and hypothetically associated functional brain network alterations. Methods: In total, 34 breast cancer patients treated with chemotherapy (BCC +), 32 patients not treated with chemotherapy (BCC −), and 35 non-cancer controls (NC) were included. Fatigue was assessed using the EORTC QLQ-C30 fatigue subscale at two time points: baseline (T1) and six months after completion of chemotherapy or matched intervals (T2). Participants also underwent resting-state functional magnetic resonance imaging (rsfMRI). An atlas spanning 90 cortical and subcortical brain regions was used to extract time series, after which Pearson correlation coefficients were calculated to construct a brain network per participant per timepoint. Network measures of local segregation and global integration were compared between groups and timepoints and correlated with fatigue. Results: As expected, fatigue increased over time in the BCC + group (p = 0.025) leading to higher fatigue compared to NC at T2 (p = 0.023). Meanwhile, fatigue decreased from T1 to T2 in the BCC − group (p = 0.013). The BCC + group had significantly lower local efficiency than NC at T2 (p = 0.033), while a negative correlation was seen between fatigue and local efficiency across timepoints and all participants (T1 rho = − 0.274, p = 0.006; T2 rho = − 0.207, p = 0.039). Conclusion: Although greater fatigue and lower local functional network segregation co-occur in breast cancer patients after chemotherapy, the relationship between the two generalized across participant subgroups, suggesting that local efficiency is a general neural correlate of fatigue.