In coral reefs, one of the great mysteries of teleost fish ecology is how larvae locate the relatively rare patches of habitat to which they recruit. The recruitment of fish larvae to a reef, after a pelagic phase lasting between 10 and 120 days, depends strongly on larval ability to swim and detect predators, prey and suitable habitat via sensory cues. However, no information is available about the relationship between brain organization in fish larvae and their sensory and swimming abilities at recruitment. For the first time, we explore the structural diversity of brain organization (comparative sizes of brain subdivisions: telencephalon, mesencephalon, cerebellum, vagal lobe and inferior lobe) among larvae of 25 coral reef fish species. We then investigate links between variation in brain organization and life history traits (swimming ability, pelagic larval duration, social behavior, diel activity and cue use relying on sensory perception). After accounting for phylogeny with independent contrasts, we found that brain organization covaried with some life history traits: (1) fish larvae with good swimming ability (>20 cm/s), a long pelagic duration (>30 days), diurnal activity and strong use of cues relying on sensory perception for detection of recruitment habitat had a larger cerebellum than other species. (2) Fish larvae with a short pelagic duration (<30 days) and nocturnal activity had a larger mesencephalon and telencephalon. Lastly, (3) fish larvae exhibiting solitary behavior during their oceanic phase had larger inferior and vagal lobes. Overall, we hypothesize that a well-developed cerebellum may allow fish larvae to improve their chances of successful recruitment after a long pelagic phase in the ocean. Our study is the first one to bring together quantitative information on brain organization and the relative development of major brain subdivisions across coral reef fish larvae, and more specifically to address the way in which this variation correlates with the recruitment process.