The technology of seed coating with superabsorbent polymer (SAP) has the potential to mitigate the negative impact of drought on seed germination and crop establishment. However, their application on the seed surface can affect the effectiveness of pesticides used for seed treatment in the protection against phytopathogens. In our work, the influence of the Aquaholder®Seed polymer coating on the effectiveness of fungicides in the protection of germinating seeds of spring barley cv. Bojos and Laudis against the fungal pathogen Bipolaris sorokiniana was studied. One-half of the seeds were first treated with fungicides, and then a polymer was applied. Fungicide efficacy was evaluated in a Petri dish test and pot test under the pathogen attack. Seed coating with SAP did not negatively affect fungicide efficacy. The percentage of germinated seeds, seedling emergence, plant height, and symptoms of the disease in the fungicide-treated variants were not significantly changed by the SAP application. Moreover, in cv. Laudis, the application of SAP alone partially protected germinating seeds against pathogen attack. The amount of pathogen DNA in plant tissues of cv. Laudis was not significantly different among seed treatments, while in cv. Bojos, the pathogen DNA increased in seeds coated with SAP alone but decreased in combined treatment with fungicides. These results demonstrated that SAP seed coating does not negatively affect the efficacy of fungicides used for seed protection against fungal pathogens.