Accurate time synchronization is fundamental to the correct and efficient operation of Wireless Sensor Networks (WSNs), especially in security-critical, time-sensitive applications. However, most existing protocols degrade substantially under malicious interference. We introduce iSTSP, an Intelligent and Secure Time Synchronization Protocol that implements a four-stage defense pipeline to ensure robust, precise synchronization even in hostile environments: (1) trust preprocessing that filters node participation using behavioral trust scoring; (2) anomaly isolation employing a lightweight autoencoder to detect and excise malicious nodes in real time; (3) reliability-weighted consensus that prioritizes high-trust nodes during time aggregation; and (4) convergence-optimized synchronization that dynamically adjusts parameters using theoretical stability bounds. We provide rigorous convergence analysis including a closed-form expression for convergence time, and validate the protocol through both simulations and real-world experiments on a controlled 16-node testbed. Under Sybil attacks with five malicious nodes within this testbed, iSTSP maintains synchronization error increases under 12% and achieves a rapid convergence. Compared to state-of-the-art protocols like TPSN, SE-FTSP, and MMAR-CTS, iSTSP offers 60% faster detection, broader threat coverage, and more than 7 times lower synchronization error, with a modest 9.3% energy overhead over 8 h. We argue this is an acceptable trade-off for mission-critical deployments requiring guaranteed security. These findings demonstrate iSTSP’s potential as a reliable solution for secure WSN synchronization and motivate future work on large-scale IoT deployments and integration with energy-efficient communication protocols.