Alveolar echinococcosis (AE) is a parasitic disease resulting from the intrahepatic growth of Echinococcus multilocularis larva. This zoonotic helminthic disease is rare but, if left untreated or treated too late, can be severe or even fatal. In France, endemic areas containing infected foxes have become larger, spreading towards western regions of the country and leading to an increased risk of environmental contamination. An observational survey was undertaken in 2014 to assess the level of knowledge of AE among primary care physicians (PCPs) and pharmacists in the Franche-Comté region. Standardized questionnaires were sent to a random sample of 183 PCPs and 236 pharmacists practicing in the Franche-Comté region (eastern France), requesting their voluntary and anonymous participation. The questionnaires collected socio-demographic details, self-evaluation and asked multiple choice questions (MCQs) about epidemiology, prevention, diagnosis and management of AE. The crude response rate was 37.5% of the PCPs and pharmacists questioned. Responses to MCQs showed that most of the participating PCPs and pharmacists had acceptable basic knowledge of AE, especially concerning epidemiology and prevention of the disease. However, a serious lack of knowledge was observed concerning the management of AE. PCPs are often the first health professionals to suspect latent AE, which is still a rural disease in France. Both PCPs and pharmacists play an important role in informing and referring patients potentially exposed to AE. This study shows that although AE is rare, PCPs and pharmacists of the Franche-Comté region have a satisfactory level of knowledge of AE.