The authors of this article analysed the impact of the COVID-19 pandemic on the financial situation of employees in small and medium-sized enterprises (SMEs) in the Czech Republic. They conducted a questionnaire survey with 251 respondents in October and November 2021. The structure of the respondents was divided according to the size of the firms, the time of operation in the market, and the focus of business activity, which was presented in detail in the tables. Statistical methods including Quadratic SVM (support vector machine) and Gaussian process regression model were used to evaluate the changes in financial valuation among employees during the pandemic. The analysis results showed that most respondents (SMEs) did not experience a difference in their financial valuation, with the most significant salary retention observed in small-sized enterprises with international operations. The statistical methods of Quadratic SVM and Gaussian process regression model contributed to a better understanding of the financial situation of employees during the pandemic. The Gaussian process confirmed that approximately 80% of the respondents did not experience any change in their salary during the pandemic. One positive finding is some small business owners and businesses that took advantage of compensation programs from the government (e.g., nursing, isolation) with positive financial outcomes for their employees. This shows that appropriately designed subsidy policies can benefit SMEs and help them survive difficult times. Overall, it can be concluded that the COVID-19 pandemic has had an impact on SMEs, some of which have been able to adapt and use state support to maintain employment and financial stability. In supporting SMEs, the government should continue to focus its strategies on maintaining jobs and providing financial support during periods of economic crises such as the pandemic. This research provides valuable insights for the formulation and implementation of effective measures to minimize the negative impacts of crises on SMEs and their employees.