Background: Homeopathy is being increasingly practiced within different medical areas of use. Homeopathic medicines are sold in German pharmacies, whereas the assortment of Swedish pharmacies does not include homeopathic medicines. Despite differences between Sweden and Germany, homeopathic medicines are classified as drugs in both countries. Objective: The aim of this study was to compare the pharmacy employees’ self-rated knowledge, use, and attitudes toward homeopathy in Sweden and Germany. Methods: A quantitative web survey was sent to 30 pharmacies in Sweden and 30 pharmacies in Germany, which were selected by using a multi-stage clustering sampling. The questionnaire contained closed-ended rating scales. To compare the self-rated knowledge, use, and attitudes toward homeopathy of Swedish and German pharmacy employees, chi-square tests and Mann-Whitney tests were performed in SPSS. Results: A total of 209 pharmacy employees answered the survey (108 in Sweden and 101 in Germany). German participants estimated their knowledge higher than the Swedish participants (p < 0.01). In both countries, most participants thought that pharmacy employees should have knowledge about homeopathy. Although most Swedish participants stated that they receive questions about homeopathy, the German pharmacy employees receive questions about homeopathy more frequently (p <0.01). Swedish participants reported less experience of own use of homeopathic medicines and less belief in their effectiveness as compared to the German participants (p < 0.01). However, in both countries, most participants stated that homeopathic medicines should be sold in pharmacies. Conclusion: As pharmacy employees should act professionally to advise customers on all drugs, increased homeopathic knowledge in pharmacy employees could potentially improve pharmaceutical practice.