The paper examines the compensation of tuition fees for Czech kindergartens (N = 1,080) during the first wave of the pandemic (spring 2020). It also analyses unpaid school fees for September and October 2020 (the second wave of Covid-19). The results revealed that due to quarantine closures the parameters of the multi-source financing of kindergartens exerted a negative impact on the multi-source financial model, which forms the basis of the management of kindergartens in the Czech decentralised regional education system. The willingness (or not) of the relevant authorities to compensate for unpaid school fees for the period of the local quarantine closure of kindergartens (or certain classes) highlighted regional inequalities in terms of the financing of preschool education during the Covid-19 pandemic.