Using real-world evidence in biomedical research, an indispensable complement to clinical trials, requires access to large quantities of patient data that are typically held separately by multiple healthcare institutions. Centralizing those data for a study is often infeasible due to privacy and security concerns. Federated analytics is rapidly emerging as a solution for enabling joint analyses of distributed medical data across a group of institutions, without sharing patient-level data. However, existing approaches either provide only limited protection of patients’ privacy by requiring the institutions to share intermediate results, which can in turn leak sensitive patient-level information, or they sacrifice the accuracy of results by adding noise to the data to mitigate potential leakage. We propose FAMHE, a novel federated analytics system that, based on multiparty homomorphic encryption (MHE), enables privacy-preserving analyses of distributed datasets by yielding highly accurate results without revealing any intermediate data. We demonstrate the applicability of FAMHE to essential biomedical analysis tasks, including Kaplan-Meier survival analysis in oncology and genome-wide association studies in medical genetics. Using our system, we accurately and efficiently reproduce two published centralized studies in a federated setting, enabling biomedical insights that are not possible from individual institutions alone. Our work represents a necessary key step towards overcoming the privacy hurdle in enabling multi-centric scientific collaborations.