Objective: Chemotherapy-related cognitive changes following breast cancer are commonly reported; however, changes in brain dynamics of large-scale neural networks remain unclear. Using data from the Aerobic exercise and CogniTIVe functioning in women with breAsT cancEr (ACTIVATE) trial, we conducted exploratory analyses to compare self-reported and objective measures of cognition and applied microstate analysis to resting state electroencephalography (EEG) data of women with breast cancer before and following chemotherapy treatment. Methods: Data from 8 female participants between the ages of 30 and 52 (mean age = 44.8 yrs, SD = 7.3 yrs) were analyzed. Cognitive function was assessed using the PROMIS (Patient-Reported Outcomes Measurement Information System) and the Trail Making Test (TMT). Five minutes of resting state, eyes-closed EEG data were also collected. Seven EEG microstates were extracted and mean microstate duration and occurrence were computed. Results: Following chemotherapy, there was a significant decrease in the PROMIS score (p = 0.003, d = 1.601), but no significant difference in the TMT. Overall, durations of microstates were significantly longer (p < 0.001, d = 2.837) and less evenly distributed following chemotherapy. The mean duration of microstate D significantly increased following chemotherapy (p = 0.007, d = 1.339). No significant correlations between microstate features and the PROMIS score were observed. Conclusions: We observed self-reported cognitive impairment and disturbed functional dynamics in the resting state brain following chemotherapy treatment. These results introduce a potential novel biomarker to evaluate the changes in large scale brain dynamics related to the cognitive effects of chemotherapy.