Background: Neck pain (NP), one of the most reported musculoskeletal disorders, is a major cause of illness and absence from university lessons among students. The COVID-19 pandemic affected higher education institutions worldwide. Academic studies shifted to online-learning, changing students’ habits and lifestyle. Data demonstrated that the pandemic and consequent lockdowns can affect people’s physical and mental well-being. Thus, the aim of this study is to evaluate the impact of COVID-19 lockdowns on the prevalence of and risk factors of NP among college students compared to the pre-epidemic period. Methods: A cross-sectional study was conducted in the form of an online questionnaire survey that included sociodemographic data, Visual Analogue Scale (VAS), Neck Disability Index (NDI), and Perceived Stress Scale (PSS). NP was reported at four time points—lifetime, last year, last six months, and current—on a scale ranging from never/seldom to almost every day. Logistic regression models were calculated for all study variables and compared to the (NDI) cut-off score of 15. Results: A total of 295 college students were recruited. Among them, 35.6% reported at least moderate neck-related disability (NDI≥15) and significantly more NP than before the lockdown. NP increased gradually and significantly (on a scale 1-4), from a lifetime mean of 1.80 to a mean of 2.57 last year to 2.73 during the past six months to the current mean of 3.07 (p< .001). Participants’ scores on the PSS were moderate, with 59.3% reporting a high level of study-related stress. Logistic regression models revealed that sitting more than three hours a day, high study-related stress and higher PSS and VAS scores were associated with higher risk of at least a moderate level of neck-related disability (R2=.513, p< .001). Conclusions: The transition from on-campus studies to online learning had negative effects on students. It significantly increased study-related stress and the development of NP. Identifying risk factors at an early stage may prevent NP from becoming chronic and affecting students’ future careers, thereby improving students’ quality of life.