Machine learning on encrypted data can address the concerns related to privacy and legality of sharing sensitive data with untrustworthy service providers, while leveraging their resources to facilitate extraction of valuable insights from otherwise non-shareable data. Fully Homomorphic Encryption (FHE) is a promising technique to enable machine learning and inferencing while providing strict guarantees against information leakage. Since deep convolutional neural networks (CNNs) have become the machine learning tool of choice in several applications, several attempts have been made to harness CNNs to extract insights from encrypted data. However, existing works focus only on ensuring data security and ignore security of model parameters. They also report high level implementations without providing rigorous analysis of the accuracy, security, and speed trade-offs involved in the FHE implementation of generic primitive operators of a CNN such as convolution, non-linear activation, and pooling. In this work, we consider a Machine Learning as a Service (MLaaS) scenario where both input data and model parameters are secured using FHE. Using the CKKS scheme available in the open-source HElib library, we show that operational parameters of the chosen FHE scheme such as the degree of the cyclotomic polynomial, depth limitations of the underlying leveled HE scheme, and the computational precision parameters have a major impact on the design of the machine learning model (especially, the choice of the activation function and pooling method). Our empirical study shows that choice of aforementioned design parameters result in significant trade-offs between accuracy, security level, and computational time. Encrypted inference experiments on the MNIST dataset indicate that other design choices such as ciphertext packing strategy and parallelization using multithreading are also critical in determining the throughput and latency of the inference process. © 2021, CC BY.