Threatened species monitoring is challenging for small, cryptic endotherms that are most effectively detected at night. Low detectability is a challenge for monitoring programmes, resulting in low statistical power and sparse or zero‐inflated datasets. To advance conservation management programmes, efforts to address this are required. In recent years thermal scanners have emerged as an effective tool for detecting small endotherms, but the diversity of available thermal tools, focal habitats and target species mean that their applicability in many key scenarios remain untested. We directly compared vehicle‐mounted thermal surveys with vehicle‐based spotlighting targeting small endotherms in Australian native grasslands. Our targets included both common species that occur at high densities, and species that are notoriously difficult to detect with spotlights, which may occur at very low densities. We completed paired surveys of roosting grassland birds, and nocturnally active small mammals at 22 sites, once using thermal scanners and once using spotlights. Ultimately, distance sampling was conducted across 136 km of transects. Thermal scanners facilitated greater detection distances and higher total detections for small endotherms when compared with spotlighting. Species of greatest conservation concern, the Plains‐wanderer (Pedionomus torquatus—Pedionomidae) and Fat‐tailed Dunnart (Sminthopsis crassicaudata—Dasyuridae) were only detected using thermal scanners. Detection distances generated for thermal scanners were reduced by higher vegetation density; however, thermal scanners continued to outperform spotlights under this scenario. Observers also detected more stationary animals and fewer birds were flushed upon detection using thermal scanners when compared with spotlighting. Thermal scanners have the potential to improve the quality of monitoring datasets by increasing detection probabilities for small endotherms. We recommend the adoption of thermal scanners as a best‐practice tool for monitoring small endotherms in open grassland habitats at night, offering new opportunities to monitor endotherms where monitoring has historically been challenging, inadequate or impossible.