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This study aimed to compare the diagnostic performance of [⁶⁸Ga]Ga-DOTA.SA.FAPi with that of [¹⁸F]F-FDG PET/CT in detecting primary and metastatic lesions of breast cancer. [¹⁸F]F-FDG and [⁶⁸Ga]Ga-DOTA.SA.FAPi PET/CT scans of histologically proven breast cancer patients were compared according to patient-based and lesion-based analysis. Forty-seven patients with a mean age of 44.8 ± 9.9 years (range: 31–66 years) were evaluated. A total of 85% of patients had invasive ductal carcinoma, and 15% had invasive lobular carcinoma. The tracer uptake [SULpeak, SULavg, and the median tumor-to-background ratio (TBR)] was significantly higher in [⁶⁸Ga]Ga-DOTA.SA.FAPi than with [¹⁸F]F-FDG PET/CT for lymph nodes, pleural metastases, and liver lesions (<i>p</i> < 0.05). However, for brain metastasis, only the median TBR was significantly higher (<i>p</i> < 0.05) compared to [¹⁸F]F-FDG. In patient-based analysis the sensitivity of [⁶⁸Ga]Ga-DOTA.SA.FAPi PET/CT was higher, but not significant than that of [¹⁸F]F-FDG PET/CT in the detection of both primary tumors and metastatic lesions. According to lesion-based analysis, on diagnostic CT, 47 patients had 44 primary tumors, 248 lymph nodes, 15 pleural, 88 liver, and 42 brain metastases. [⁶⁸Ga]Ga-DOTA.SA.FAPi scan identified more abnormal lesions than [¹⁸F]F-FDG in all the primary and metastatic sites with a maximum marked difference in the primary site [88.6% vs. 81.8%; <i>p</i>-0.001], lymph nodes [89.1% vs. 83.8%; <i>p</i>-0.0001], pleural metastases [93.3% vs. 73%; <i>p</i>-0.096] and brain metastasis [100% vs. 59.5%; <i>p</i>-0.0001]. [⁶⁸Ga]Ga-DOTA.SA.FAPi PET/CT was superior to [¹⁸F]F-FDG PET/CT in the imaging of breast cancers.