Homeopathy is 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. The aim of this study was to compare pharmacy employees’ knowledge, use and attitudes toward homeopathy in Sweden and Germany. A quantitative web-survey was send to 30 pharmacies in Sweden and 30 pharmacies in Germany. To compare knowledge, use and attitudes toward homeopathy of Swedish and German pharmacy employees, chi-square tests and Mann-Whitney tests were performed in SPSS. A total of 209 pharmacy employees answered the survey (108 in Sweden and 101 in Germany). German participants estimated their knowledge higher than 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, 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 believe in their effectiveness compared to German participants (p < 0.01). However, in both countries, most participants stated that homeopathic medicines should be sold in pharmacies. As pharmacy employees should act professionally to advice customers on all drugs, increased homeopathic knowledge in pharmacy employees could potentially improve pharmaceutical praxis. If homeopathic medicines should be sold in pharmacies or not remains a discussion issue that could be addressed in future studies.