In a period globally known as long COVID, several post-acute infection sequelae and vaccination effects have been discussed. Objectives: This study aimed to identify the effects of COVID-19 infection and vaccines on the menstrual cycle of adolescents attending higher education and to verify the association between personal health factors and changes in their menstrual cycle after contact with the virus SARS-CoV-2 via infection or via the vaccine. Methods: A cross-sectional study was conducted using a questionnaire for data collection, applied online to Portuguese higher education adolescents aged between 18 and 24. The sample included 401 individuals. The statistical analysis of data was performed using SPSS. Results: More than half of the sample had a COVID-19 infection only once and took two doses of the vaccine. The mRNA Comirnaty 30 µg BioNTech vaccine was administered to 73.1%. The most common menstrual changes were an increase in blood clots, the blood becoming darker, shorter menstrual cycles, scarcer blood flow, and more irregular cycles. Menstrual changes correlated significantly with vaccination but not with infection. Conclusions: This study showed a lower percentage of women affected than other studies carried out closer to the pandemic period, which could mean that the effects are diminishing over time. Thus, adolescents’ menstrual health should be monitored.