Septoria melissae Desm., the most important pathogen of lemon balm (Melissa officinalis) occurs each year on plantations. The fungus may cause serious yield losses in the absence of proper plant protection. Breeding resistant or tolerant cultivars could play an important role in plant protection of medicinal plants. However, only a few descriptions of tolerant varieties of lemon balm are available. The goal of this work was to evaluate the susceptibility of three accessions of M. officinalis against the pathogen of Septoria leaf spot under field conditions at Budapest-Soroksár (Hungary) in 2017–2018. Differences in susceptibility of the accessions were observed in both years. The accession of M. officinalis subsp. altissima proved to be the least susceptible to Septoria infection. The frequency of the infected leaves was only 5.1 and 28.1% in 2017 and 2018, respectively. However, the cultivar M. officinalis subsp. officinalis ‘Lorelei’ turned out to be the most susceptible to the pathogen with an average infection level of 26.1 and 66.6%, 1.3–6.1 times higher than that of the other accessions in each year, respectively. Development of disease tolerant M. officinalis cultivars may be an effective tool in the plant protection of lemon balm.