Island restoration projects that address invasive species issues require measures of invader populations before eradication or control efforts begin, especially for cryptic species such as introduced rodents. To address this need, we tested a non-invasive technique for measuring inter-annual variation in Norway rat (Rattus norvegicus) activity at Kiska Island, Aleutian Islands, Alaska, during 2005-2010. Snap-trapping could not be used at a large mixed colony of small seabirds (auklets, Aethia spp.) at Sirius Point, Kiska, due to the certainty of bird mortality. Away from the colony site at Kiska Harbour, in June 2005, we used snap-traps to measure capture rates, and found a similar corrected trap index (8.5 captures/100 trap nights) to that recorded pre-eradication at Langara Island, British Columbia (8.2 captures/100 trap nights). At Sirius Point, we determined the most effective rat-monitoring method to be a series transects spanning the auklet colony, with detection stations set at 25 m intervals, each including a baited wax block. Rat detections varied nearly 100-fold among years, suggesting high inter-annual variability in the rat population. We found no statistically significant relationship between our rat index and auklet breeding success at Sirius Point with our small sample of years (n = 5, 2006–2010). Nevertheless, we believe rat numbers were much lower at Sirius Point during 2006–2010 than observed qualitatively during 2001–2002 when auklets experienced breeding failure. Our rat activity index protocol is likely applicable to other situations in which introduced rodent numbers needs to be monitored while safeguarding native fauna that could be harmed by snap-trapping.