The blue-tailed skink (Cryptoblepharus egeriae) is endemic to Christmas Island but underwent rapid population declines in the 1990s and 2000s and was listed as Extinct in the Wild in 2017. As invasive giant centipedes (Scolependra subspinipes) were implicated as a cause of a failed reintroduction of captive bred skinks into a fenced enclosure, we undertook a mesocosm experiment to investigate if skink survival and body condition was negatively affected by the presence and density of S. subspinipes. In addition, we used DNA barcoding to determine if wild centipedes consume other reptile species on Christmas Island. In the mesocosm experiments, survival of skinks was reduced by 30% and 44% at low and high centipede densities respectively over 12 weeks, and skink body condition also declined significantly over this period. DNA barcoding confirmed that skinks that were lost during the mesocosm experiment had been consumed by centipedes. Further, we detected DNA of two invasive reptiles (the common wolf snake Lycodon capucinus and the Asian House gecko Hemidactylus frenatus) in the stomachs of wild-caught centipedes, suggesting that centipedes are a generalist predator of reptiles in this island ecosystem. Based on these results, we recommend that attempts to reintroduce C. egeriae to Christmas Island should include the control of centipedes to increase the likelihood of success.