Breast cancer (BC) is a heterogeneous disease with high metastasis potential, especially in the bones, liver, and lungs. Circulating tumor cells (CTCs), which emerge from active tumors, represent an early step toward metastasis and are associated with poor prognosis. CTCs of carcinoma origin are believed to express EpCAM and cytokeratins (CKs), common epithelial markers that are frequently used to identify them. However, in practice, the most aggressive CTCs lose the expression of those markers, leading to the partial loss of important information. Thus, finding some novel markers that identify CTCs regardless of their heterogeneity is crucial. A specific bioinformatics workflow integrating primary tumor and diverse BC cell lines transcriptomic expression analysis was developed and compared with single CTC transcriptomic analyses. We have identified a set of genes that are overexpressed in primary BC cells and are commonly upregulated among BC cell lines. Fifty of them were also found to be expressed in BC CTCs by single-cell transcriptomic analysis. Further in silico sorting narrowed this list to 12 genes. Using ScreenCell technology to isolate cancer cells spiked into normal blood, we tested the protein expression of all corresponding genes in vitro using the double immunocytochemistry method and validated MARCKSL1, SLC9A3R1, and RHOD as the most expressed markers. We then isolated the CTCs of 40 LN-invaded BC patients and 18 healthy donors using ScreenCell technology and showed that the combination of these three markers resulted in significantly better recognition of CTCs compared to EpCAM and CK conventional markers. Employing these novel markers, we found a clear distinction between blood samples from patients and healthy donors. In conclusion, through a specific bioinformatics workflow, in addition to in vitro and further clinical validations, we found three novel markers to precisely identify CTCs. These markers, when used together, enable a significantly more efficient identification of CTCs compared to conventional epithelial markers.