Over the past two decades, circulating tumor cells (CTCs) have been widely recognized for their importance in clinical trials. While most enrichment methods for these cells have been conducted through the batch process due to their rarity in blood and the need for large sample volumes, the batch process leads to unavoidable cell loss. Given the heterogenetic features of CTCs, this cell loss may limit the validity of research that relies on the isolation of CTCs; such research includes cancer prognosis, diagnosis of minimal residual diseases, assessment of tumor sensitivity to anticancer drugs, and the personalization of anticancer therapies. Recent advances in microfluidic approaches have made it possible to enrich CTCs with a small degree of cell loss. In this review, we highlight several microfluidic-based positive and negative enrichment methods that are the subject of considerable research interest (e.g. EpCAM-dependent assay and EpCAM-independent assay) and suggest a microfluidic-based single cell analysis platform for the down-stream analysis of CTCs. We also discuss critical concerns and future directions for research.