Coral reef fish larvae use sound to find suitable habitat during their vital settlement stage. Yet boat noise, which can cause stress and avoidance behaviour, and may cause masking via reduction of perceptual space, is common around coral islands and continental shelf habitats due to boat activity associated with fishing, tourism and transport of passengers and cargo. In a choice chamber experiment with settlement-stage coral reef fish larvae of the species Apogon doryssa, the directional responses of larvae were tested to 5 different noise types: Reef, Reef+Boat, Ocean, Ocean+Boat and White noise. The results showed that 69% of fish swam towards Reef playback compared with only 56% during Reef+Boat playback, while 44% of fish larvae moved away from Reef+Boat playback compared to only 8% during Reef playback. Significant directional responses were not observed during White noise, Ocean noise or Ocean+Boat noise playback. Overall, this study suggests that anthropogenic noise could have a disruptive effect on the response of fish larvae to natural reef sound, with implications for settlement and population dynamics in coral reef habitats disturbed by boat traffic.