Recently, unmanned aerial vehicles (UAVs) have emerged as a viable solution for data collection from remote Internet of Things (IoT) applications. However, the successful implementation in this regard necessitates the development of a reliable and energy-efficient routing protocol. This paper proposes a reliable and an energy-efficient UAV-assisted clustering hierarchical (EEUCH) protocol designed for remote wireless sensor networks (WSNs) based IoT applications. The proposed EEUCH routing protocol facilitates UAVs to collect data from ground sensor nodes (SNs) that are equipped with wake-up radios (WuRs) and deployed remotely from the base station (BS) in the field of interest (FoI). During each round of the EEUCH protocol, the UAVs arrive at the predefined hovering positions at the FoI, perform clear channel assignment, and broadcast wake-up calls (WuCs) to the SNs. Upon receiving the WuCs by the SNs’ wake-up receivers, the SNs perform carrier sense multiple access/collision avoidance before sending joining requests to ensure reliability and cluster-memberships with the particular UAV whose WuC is received. The cluster-member SNs turn on their main radios (MRs) for data packet transmission. The UAV assigns time division multiple access (TDMA) slots to each of its cluster-member SNs whose joining request is received. Each SN must send the data packets in its assigned TDMA slot. When data packets are successfully received by the UAV, it sends acknowledgments to the SNs, after which the SNs turn off their MRs, completing a single round of the protocol. The proposed EEUCH routing protocol with WuR eliminates the issue of cluster overlapping, improves the overall performance, and increases network stability time by a factor of 8.7. It also improves energy efficiency by a factor of 12.55, resulting in a longer network lifespan compared to Low Energy Adaptive Clustering Hierarchy (LEACH) protocol. Moreover, EEUCH collects 5.05 times more data from the FoI than LEACH. These results are based on simulations in which the EEUCH protocol outperformed the existing six benchmark routing protocols proposed for homogeneous, two-tier, and three-tier heterogeneous WSNs.