(1) Background: The recent epidemiological events were high-stress level generators for humanity, particularly for pregnant women, influencing their attitude, behavior, and decisions regarding vaccination during pregnancy or regarding their future child. The aim of this study was to analyze the anti-pertussis vaccination decision-shaping factors in pregnant women during two epidemiological periods: the measles epidemic and the COVID-19 pandemic. (2) Methods: Two groups of pregnant women were invited to be part of a medical education program, having as the main theme the infectious disease risks and their prevention through vaccination. Before launching the program, participants received a 12-item questionnaire. From a total number of 362 pregnant women enrolled in the study, 182 participated in 2019, and 180 participated in 2022. (3) Results: The socio-demographic data revealed that the age of pregnant women participating in medical education programs increased in 2022 by 1.7 years (p < 0.01). In vitro fertilization was reported in a significantly higher proportion (20% in 2022 vs 9.8% in 2019, p < 0.01). Participation in community-initiated educational programs almost doubled during the pandemic time from 18.7% in 2019 to 33.9% in 2022 (p < 0.01). Pertussis vaccine acceptancy (VA) dropped from 85% in 2019 to 44.4% in 2022 (p < 0.01) (4) Conclusions: In this study, we reported fast-growing vaccine hesitancy and severe declared vaccine reluctance. The results of this complex long-term study, which evaluated pregnant women over several years, showed a five-fold increase in the percentage of pregnant women who disagreed with personal pertussis vaccination. This draws attention to the risks of pertussis epidemic outbreaks in pregnant women and their future infants in the first couple of months of life before the initiation of vaccination.