The preservation of privacy during a search has become a serious problem in recent years. There is an increasing requirement to ensure that user queries are not abused by a third party, including the search provider. Fully homomorphic encryption (FHE) can conduct addition and multiplication directly over ciphertext. Using FHE, privacy, concerning both the user queries and the database of the search provider, can be protected. In this paper, we propose a privacy-preserving query system model. We implemented the proposed model in a real-world medicine side-effect query system. We applied a filtering technique, prior to the query deployment, to reduce the size of the database and used multi-threading to accelerate the search. The system was tested 10,000 times with a random query, using a database comprising 40,000 records of simulation data, and completed 99.84% of the queries within 60 seconds (s), proving the real-world applicability of our system.