Background Shoulder stiffness is a common health issue in Japan. During the COVID-19 pandemic, people were forced to stay home which possibly escalated the development of shoulder stiffness. We aimed to assess associations of lifestyle changes and newly developed neck and shoulder pain (NSP) during the pandemic. Methods A cross-sectional study was conducted, analyzing the data from the Japan COVID-19 and Society Internet Survey (JACSIS), an internet survey conducted from August to September 2020. Data included sociodemographic, lifestyle and health measures related to NSP during the pandemic. Multivariable logistic regression models were fitted to calculate adjusted odds ratio (AOR) with 95% confidence interval (CI) for newly developed NSP with adjustment for lifestyle, physiological and psychosocial changes. Results After exclusion of participants with existing pain, 25,482 participants (12,673 male, 12,809 female) aged 15-79 years were included in the analysis. Of these, 4.1% reported newly developed NSP. Weight gain and long sedentary time were strongly associated with the NSP (AOR (95%CI): 2.4 (2.0-2.8) and 1.81 (1.4-2.3)). Stratified analyses of 1,751 students and 4,211 teleworkers showed significant associations (AOR (95%CI): 2.1 (1.4-2.8) and 2.5 (1.9-3.2)) compared to non-workers and non-teleworkers, respectively. Conclusions Students and teleworkers became prone to NSP during the pandemic. However, factors which were associated to pain did not differ during the pandemic compared with the previous studies. Key messages Preventive measures for NSP should be taken in students and teleworkers.