Blood- and neuroimaging-based indicators can change as a result of breast cancer treatment. For breast cancer survivors, a summary of the prognostic usefulness of these markers for cognition is missing. Following PRISMA guidelines, this systematic review summarised studies from the previous ten years that used the PubMed database to assess blood markers and the relationship between blood- or structural neuroimaging markers and cognition throughout the chemotherapy trajectory for primary breast cancer. There were 44 studies total. All blood marker categories showed variations from the start of chemotherapy to years after the end of the treatment. White and grey matter measurements in frontal, temporal, and parietal brain areas were linked to cognitive functioning, as were blood indicators (mostly inflammation-related) during, shortly after, or years postchemotherapy. There is preliminary evidence that epigenetic and metabolic changes only occur after chemotherapy and are related to cognition. This review showed temporally dependent relationships between particular blood-based and structural neuroimaging indicators and cognitive impairment in breast cancer patients. Further research on predicting the long-term cognitive consequences of chemotherapy is recommended to use both neuroimaging- and blood markers (such as those of neural integrity, epigenetics, and metabolism.