In this study, a structural health monitoring (SHM) fastener consisting of a conformable eddy current sensor film that is integrated with a metallic sleeve that goes around the fastener shank was developed for in situ monitoring of fatigue cracks at hole locations in layered metallic joints. Integration of sensors with the fastener shank is an optimal methodology for embedding sensors to detect cracks, which most commonly initiate at bolt-hole boundaries in metallic airframe components. The sensors are located in proximity to the bolt-hole boundary through the entire joint stack up, enabling detection of cracks on inner joint layers, which are otherwise inaccessible and cannot be detected with traditional surface-mounted SHM technologies. An additive, interleaved, multilayered, electromagnetic (AIME) sensor was designed for this application. The sensor's salient qualities are an enhanced capability to inspect adjacent joint layers with high degrees of liftoff, or separation between sensor and joint layer, and a capability to track cracks out to great depth as they propagate from a through-hole boundary. The analysis and design of the sensor film and sensor/fastener system are presented herein followed by an experimental validation of the complete SHM system.