Stingrays are thought to play important ecological roles in coral reef ecosystems. However, little is known about juvenile stingray movement patterns and habitat use in coral reefs. This study used active acoustic telemetry to determine fine-scale diel movement patterns and habitat use of juvenile cowtail stingrays (Pastinachus ater) in a coral reef flat environment. Seven cowtail stingrays (4 males and 3 females) were manually tracked between April and December 2016. Each individual was tracked over 2 days, generating a total of 14 active tracks ranging from 4.91 to 9 h. Specimens moved at an average speed of 2.44 m min-1 ± 0.87 SE, with minimum distances travelled ranging from 546 to 1446 m. Tracking data showed that juvenile cowtail stingrays move in response to tidal cycles, moving faster and in straighter pathways during incoming and outgoing tides. Juvenile cowtail stingrays also showed a strong affinity to sand flat areas and mangrove edge areas. These areas provide food resources and potential refuges for juvenile rays to avoid predators. Coral reef flats were identified as secondary refuge for juveniles during the lowest tides. Future research is necessary to fully unveil the major drivers of juvenile cowtail stingray seasonal and ontogenetic movement patterns and habitat use within coral reef flat environments. This information is important to establish a full understanding of juvenile cowtail stingray ecology, but could also improve management and conservation policies.