Amyotrophic lateral sclerosis (ALS) with only motor impairment (ALS-pure motor) and the behavioral variant of frontotemporal dementia (bvFTD) are hypothesized to represent extreme ends of a disease spectrum, which encompasses ALS with cognitive/behavioral impairment (ALSci/bi). In this longitudinal magnetoencephalography (MEG) study, we investigated changes in brain network topology of ALSci/bi over time as compared with ALS-pure motor and bvFTD patients. Resting-state MEG was recorded in ALS-pure motor (n = 9), ALSci/bi (n = 16), and bvFTD (n = 16) at baseline and 5-month follow-up, projected to source space. The corrected version of the amplitude envelope correlation was applied to compute frequency-band-specific functional connectivity between brain regions, from which the backbone of the functional networks was constructed using the minimum spanning tree (MST) approach. Reference MSTs were computed based on the functional connectivity matrices for ALS-pure motor and bvFTD, against which the networks of ALSci/bi were compared. We showed that, at baseline, networks in the theta band of ALSci/bi patients were more similar to ALS-pure motor than bvFTD. At follow-up, ALSci/bi patients’ beta-band network similarity had moved away from ALS-pure motor and resembled bvFTD. In conclusion, our findings suggest that brain networks of ALSci/bi patients move along the ALS-bvFTD spectrum over time, from ALS-pure motor to bvFTD-like topology.