Invasive geckos of the genus Hemidactylus (Gekkonidae) are spreading rapidly through urban environments in many tropical and subtropical parts of the world. The invaders have caused rapid declines in native gecko abundance in some areas, but their interactions with Australian native species remain unknown. In a small rural village near Darwin, we found that Hemidactylus frenatus is abundant around both lighted and unlighted buildings, but rarely found in surrounding bushland. It is sympatric with the larger Gehyra australis (Gekkonidae) in this disturbed site, and often forages on the same buildings, but is active mostly during the dry-season (vs. wet-season for G. australis) and is competitively subordinate to the larger native species. In laboratory encounters, H. frenatus fled from G. australis, and modified its refuge-site use in the presence of the native lizard. In those same trials, the native gecko often attacked and rarely fled; and did not shift its refuge-site selection. In field surveys, the two taxa frequently co-occurred. However, substrate use of the invasive H. frenatus was modified by the presence of the native G. australis, consistent with competitive displacement. Our counts of H. frenatus were highest during the dry-season, when G. australis (like most other small native reptiles) is relatively inactive. The invasive gecko thus appears to be exploiting a ‘vacant niche’ around buildings, rather than displacing the native gecko taxon. This outcome may reflect the size disparity between the native species and the invader; Hemidactylus frenatus may well have significant ecological impacts on smaller native lizards.