This cross-sectional study assessed prenatal pertussis vaccination acceptance in Taiwan. A sample of pregnant women from five private clinics in Taiwan was recruited. Demographics, experience of prenatal vaccinations, key considerations, knowledge, and attitude about pertussis and its vaccination were measured. Among 505 participants, the vaccination rate, including planned vaccination, was 29.7%. Factors associated with acceptance included clinic location, primary caregiver of the newborn, newborns with siblings, previous influenza vaccination history, knowledge and attitude toward pertussis and its vaccination. Public health agencies should provide free vaccinations, clarify misinformation, and publicize prevention information, to improve prenatal pertussis vaccination acceptance.