Single circulating tumor cell (sCTC) analysis enables the determination of predominant CTC phenotypes and genotypes. We previously demonstrated the feasibility of sCTC detection and genomic characterization in high-grade serous ovarian cancer (HGSOC) by combining immune-magnetic enrichment and image-based sorting, followed by whole-genome amplification (WGA) and next-generation sequencing-based copy number alteration analysis (CNA). Here we aimed to improve our workflow by incorporating HGSOC-specific markers, folate receptor alpha (FRα), and markers to identify epithelial (cytokeratin) and mesenchymal (vimentin) phenotypes for the phenotypic as well as genotypic analysis of sCTCs over the course of treatment in 42 HGSOC patients. We detected a significant reduction of FRα-positive cells (P = 0.0205) and an expansion of cells with a high nuclear staining and no target antigen expression (P = 0.002). Before treatment, sCTCs showed an enrichment in CNAs of Chromosomes 2, 7, and 12, while CNA dynamics of sCTCs suggested a potential selection of distinct CNAs specific to the homologous recombination pathway. sCTCs revealed persistent CNAs in the CDK4 and emerging ones in the ALK oncogene. Notably, primary tumors revealed considerable fractions of shared genomic aberrations.