Objectives: Cancer-related fatigue (CRF) is highly prevalent in patients with breast cancer, resulting in undesirable outcomes and even reduced survival rates. This cross-sectional study investigated the relationship between dietary quality and CRF in patients with breast cancer, and the potential role of gut microbiota (GM) in this association. Methods: Dietary intake and CRF were evaluated in 342 patients, with 64 fecal samples collected for 16sRNA sequencing and 106 plasma samples for tryptophan (TRP) metabolite determination. Results: A total of 149 (43.6%) patients experienced CRF, which was significantly associated with low intakes of protein, vitamin A, vitamin E, dietary fiber, phosphorus, magnesium, potassium, iron, and copper (p < 0.05), and a remarkably low Chinese Healthy Eating Index (CHEI) score (p < 0.05). CRF patients had decreased GM diversity, an unhealthier GM composition, lower TRP concentrations, and a higher kynurenine (KYN)/TRP ratio (p < 0.05). Mediation analyses revealed that both the Sobs index (ACME = −0.0005; 95% CI −0.0051, −0.0001; p = 0.034) and the Chao index (ACME = −0.0005; 95% CI −0.0050, −0.0001; p = 0.033) were significant mediators of the correlation between total CHEI score and CRF. Conclusions: The presence of CRF in patients with breast cancer might be correlated with inadequate nutrient intake and low dietary quality via GM-dependent pathways.