To prevent the spread of coronavirus disease 2019 (COVID-19), desk workers in Japan have been encouraged to work from home. Due to rapidly increased working from home, working in environments that are not properly designed and working with poor posture can affect low back pain (LBP). This study aimed to examine the relationship between increased work from home during the COVID-19 pandemic and LBP among Japanese desk workers. Using study data from the Japan COVID-19 and Society Internet Survey 2020 conducted from August to September 2020, 4227 desk workers who did not have LBP before the COVID-19 pandemic were analyzed out of 25,482 total respondents. Odds ratios (ORs) and 95% confidence intervals (CIs) for LBP were calculated by multivariable logistic regression, adjusting for covariates such as socioeconomic factors. During the COVID-19 pandemic, 31.3% of desk workers with an increased chance of working from home, and 4.1% had LBP. Desk workers with increased working from home were more likely to have LBP (OR: 2.00 (95% CI, 1.36-2.93)). In this large-scale study, increased work from home was associated with LBP among desk workers during the COVID-19 pandemic. Therefore, preparing an appropriate work environment for desk workers working from home can improve productivity, leading to positive effects.