Machine Learning (ML) techniques now impact a wide variety of domains. Highly regulated industries such as healthcare and finance have stringent compliance and data governance policies around data sharing. Advances in secure multiparty computation (SMC) for privacy-preserving machine learning (PPML) can help transform these regulated industries by allowing ML computations over encrypted data with personally identifiable information (PII). Yet very little of SMC-based PPML has been put into practice so far. In this paper we present the very first framework for privacy-preserving classification of tree ensembles with application in healthcare. We first describe the underlying cryptographic protocols that enable a healthcare organization to send encrypted data securely to a ML scoring service and obtain encrypted class labels without the scoring service actually seeing that input in the clear. We then describe the deployment challenges we solved to integrate these protocols in a cloud based scalable risk-prediction platform with multiple ML models for healthcare AI. Included are system internals, and evaluations of our deployment for supporting physicians to drive better clinical outcomes in an accurate, scalable, and provably secure manner. To the best of our knowledge, this is the first such applied framework with SMC-based privacy-preserving machine learning for healthcare. © 2018 IEEE.