Cellular heterogeneity is a major hindrance, leading to the misunderstanding of dynamic cell biology. However, single cell analysis (SCA) has been used as a practical means to overcome this drawback. Many contemporary methodologies are available for single cell analysis; among these, microfluidics is the most attractive and effective technology, due to its advantages of low-volume specimen consumption, label-free evaluation, and real-time monitoring, among others. In this paper, a conceptual application for microfluidic single cell analysis for veterinary research is presented. A microfluidic device is fabricated with an elastomer substrate, polydimethylsiloxane (PDMS), under standard soft lithography. The performance of the microdevice is high-throughput, sensitive, and user-friendly. A total of 53.1% of the triangular microwells were able to trap single canine cutaneous mast cell tumor (MCT) cells. Of these, 38.82% were single cell entrapments, while 14.34% were multiple cell entrapments. The ratio of single-to-multiple cell trapping was high, at 2.7:1. In addition, 80.5% of the trapped cells were viable, indicating that the system was non-lethal. OCT4A-immunofluorescence combined with the proposed system can assess OCT4A expression in trapped single cells more precisely than OCT4A-immunohistochemistry. Therefore, the results suggest that microfluidic single cell analysis could potentially reduce the impact of cellular heterogeneity.