Propolis contains many effective antifungal compounds that have not yet been identified and evaluated. In addition, distinguishing samples of propolis with high antifungal activity from less active ones would be beneficial for effective therapy. Propolis samples were collected from four different geographical regions in Hungary and used to prepare ethanol extracts for analysis. First, an antifungal susceptibility test was performed on Candida albicans. Then, gas chromatography-mass spectrometry (GC-MS) and an opto-electronic nose were applied for the classification of propolis samples. In three propolis samples, the IC₅₀ was measured between 72 and 134 µg/mL, but it was not calculable in the fourth sample. GC-MS analysis of the four propolis samples identified several compounds belonging to the various chemical classes. In the antifungal samples, the relative concentration of 11,14-eicosadienoic acid was the highest. Based on the opto-electronic electronic nose measurements, 98.4% of the original grouped antifungal/non-antifungal cases were classified correctly. We identified several molecules from propolis with potential antifungal properties. In addition, this is the first report to demonstrate the usefulness of a portable opto-electronic nose to identify propolis samples with high antifungal activity. These results may contribute to the rapid and efficient selection of new fungicide-candidate molecules and effective propolis samples for treatment.