While female participation in the labor market is crucial for women’s empowerment, studies focusing on gender bias in enterprise employment are limited. The present study investigates the determinants of female participation in Vietnamese enterprises from 2011 to 2015. The Feasible Generalized Least Squares (FGLS) method was used to analyze data from a survey of Vietnamese micro-, small-, and medium-sized enterprises. The study also conducted the Oaxaca–Blinder decomposition to assess the degree of discriminatory treatment existing in firms in the male-intensive sector compared with that in the female-intensive sector. The results indicate that export activity, human capital investment, industry characteristics, length of operation, firm size, gender, and business owners’ social capital have positive effects on female participation in enterprises. Contrarily, labor remuneration and the level of capital per worker show a negative correlation. Gender discrimination explains 26.11% of the number of female employees and 87.78% of the difference in female workers’ proportion.