According to recent security analysis reports, malicious software (a.k.a. malware) is rising at an alarming rate in numbers, complexity, and harmful purposes to compromise the security of modern computer systems. Recently, malware detection based on low-level hardware features (e.g., Hardware Performance Counters (HPCs) information) has emerged as an effective alternative solution to address the complexity and performance overheads of traditional software-based detection methods. Hardware-assisted Malware Detection (HMD) techniques depend on standard Machine Learning (ML) classifiers to detect signatures of malicious applications by monitoring built-in HPC registers during execution at run-time. Prior HMD methods though effective have limited their study on detecting malicious applications that are spawned as a separate thread during application execution, hence detecting stealthy malware patterns at run-time remains a critical challenge. Stealthy malware refers to harmful cyber attacks in which malicious code is hidden within benign applications and remains undetected by traditional malware detection approaches. In this paper, we first present a comprehensive review of recent advances in hardware-assisted malware detection studies that have used standard ML techniques to detect the malware signatures. Next, to address the challenge of stealthy malware detection at the processor’s hardware level, we propose StealthMiner, a novel specialized time series machine learning-based approach to accurately detect stealthy malware trace at run-time using branch instructions, the most prominent HPC feature. StealthMiner is based on a lightweight time series Fully Convolutional Neural Network (FCN) model that automatically identifies potentially contaminated samples in HPC-based time series data and utilizes them to accurately recognize the trace of stealthy malware. Our analysis demonstrates that using state-of-the-art ML-based malware detection methods is not effective in detecting stealthy malware samples since the captured HPC data not only represents malware but also carries benign applications’ microarchitectural data. The experimental results demonstrate that with the aid of our novel intelligent approach, stealthy malware can be detected at run-time with 94% detection performance on average with only one HPC feature, outperforming the detection performance of state-of-the-art HMD and general time series classification methods by up to 42% and 36%, respectively.