Purpose The aim of this study was to investigate the effect of working from home on neck pain (NP) among office workers during the COVID-19 pandemic. Methods Participants from two Swiss organisations, aged 18–65 years and working from home during the lockdown (n = 69) were included. Baseline data collected in January 2020 before the lockdown (office work) were compared with follow-up data in April 2020 during lockdown (working from home). The primary outcome of NP was assessed with a measure of intensity and disability. Secondary outcomes were quality of workstation ergonomics, number of work breaks, and time spent working at the computer. Two linear mixed effects models were fitted to the data to estimate the change in NP. Results No clinically relevant change in the average NP intensity and neck disability was found between measurement time points. Each working hour at the computer increased NP intensity by 0.36 points (95% CI: 0.09 to 0.62) indicating strong evidence. No such effect was found for neck disability. Each work break taken reduced neck disability by 2.30 points (95% CI:  − 4.18 to  − 0.42, evidence). No such effect was found for NP intensity. There is very strong evidence that workstation ergonomics was poorer at home. Conclusion The number of work breaks and hours spent at the computer seem to have a greater effect on NP than the place of work (office, at home), measurement time point (before COVID-19, during lockdown) or the workstation ergonomics. Further research should investigate the effect of social and psychological factors. Trial registration ClinicalTrials.gov, NCT04169646. Registered 15 November 2019—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT04169646.

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