Abstract Background Gender-biased discrimination and preferences are global phenomena, particularly son preferences. However, updated evidence about this issue in Vietnam has not yet been provided. Therefore, this study aimed to examine the gender preferences among pregnant women and identify associated factors of such preferences. Methods A cross-sectional survey was conducted in two hospitals in Vietnam with 732 pregnant women. Gender preferences for their child were asked, along with socio-demographic (e.g., education, occupation) and pregnancy characteristics (e.g., pressure to have a son, gender of first child, the importance to have a son of family members, and information sources on pregnancy care) by using face-to-face interviews and a structured questionnaire. Multinomial logistic regression was performed to determine factors associated with gender preferences. Results About 51.9% of the participants had no gender preference, while, among those who had a gender preference, 26.5% preferred sons, and 21.6% preferred daughters. Only 6.2% had pressure to have a son. Having the first child who was female (OR = 4.16, 95%CI = 1.54–11.25), having the pressure to have a son (OR = 6.77, 95%CI = 2.06–22.26), and higher self-perceived importance to have a son (OR = 3.05, 95%CI = 1.85–5.02) were positively associated with son preference. Otherwise, women having partners with high school education or above (OR = 2.04, 95%CI = 1.06–3.91), living with parents-in-law (OR = 2.33; 95%CI = 1.25–4.34), the higher number of pregnancies, and a higher degree of importance in having a son regarding parents-in-law (OR = 2.15, 95%CI = 1.38–3.35) associated with higher odds of preferring daughter. Conclusion This study showed that gender preference was common among pregnant women, but the pressure to have a son was low. Further education programs and legal institutions should be implemented to improve gender inequality and gender preference in society.