Cell sorting via flow cytometry is a powerful tool to select subpopulations of cells in many biological fields. Selection of fertilisation-prone sperm is a critical step to ensure a stable and high fertilisation rate in in vitro fertilisation (IVF). However, a combination of conventional cell sorting and IVF system has not been established because of severe mechanical damages to the sperm during the sorting process. A cell sorter with microfluidics chip technology that lessens cell damage during cell sorting may address this problem. We evaluated the effects of microfluidics chip cell sorting on the sperm using the parameters, such as motility and fertility, and found this cell sorting method had minimal harmful effect on the sperm. Then, sperm were selected by a marker for acrosome reaction and showed higher fertilisation rate than that of the population of acrosome-intact sperm. Embryo derived from these sperm developed normally. These results indicated that microfluidics chip cell sorting can select fertile sperm to improve IVF technique.