Wastewater-based epidemiology (WBE) is one of the most promising approaches to effectively monitor the spread of COVID-19. The virus concentration in faeces and its temporal variations are essential information for WBE. While some clinical studies have reported SARS-CoV-2 concentrations in faeces, the value varies amongst patients and changes over time. The present study aimed to examine how the temporal variations in the concentration of virus in faeces affect the monitoring of disease incidence. We reanalysed the experimental findings of clinical studies to estimate the duration of virus shedding and the faecal virus concentration. Available experimental data as of 23 October 2020 were collected. The viral shedding kinetics was modelled, and the dynamic model was fitted to the collected data by a Bayesian framework. Using posterior distributions, the duration of viral shedding and the concentration of virus copies in faeces over time were computed. We estimated the median concentration of SARS-CoV-2 in faeces as 3.4 (95% CrI: 0.24–6.5) log copies per gram-faeces over the shedding period, and our model implied that the duration of viral shedding was 26.0 days (95% CrI: 21.7–34.9), given the current standard quantification limit (Ct = 40). With simulated incidences, our results also indicated that a one-week delay between symptom onset and wastewater sampling increased the estimation of incidence by a factor of 17.2 (i.e., 101.24 times higher). Our results demonstrated that the temporal variation in virus concentration in faeces affects microbial monitoring systems such as WBE. The present study also implied the need for adjusting the estimates of virus concentration in faeces by incorporating the kinetics of unobserved concentrations. The method used in this study is easily implemented in further simulations; therefore, the results of this study might contribute to enhancing disease surveillance and risk assessments that require quantities of virus to be excreted into the environment. Display omitted •SARS-CoV-2 is excreted in faeces, but its time course has been understudied.•SARS-CoV-2 concentration in faeces re-analysed using a kinetic viral shedding model•The duration of viral shedding was estimated to be 20–32 days.•Median concentration was 2.6 log copies/g of faeces over the shedding period.•WBE needs to consider temporal variations in viral concentrations in faeces.