Periodic patterns make up a variety of tissues, including skin appendages such as feathers and scales. Skin appendages serve important and diverse functions across vertebrates, yet the mechanisms that regulate their patterning are not fully understood. Here, we have used live imaging to investigate dynamic signals regulating the ontogeny of zebrafish scales. Scales are bony skin appendages which develop sequentially along the anterior-posterior and dorsal-ventral axes to cover the fish in a hexagonal array. We have found that scale development requires cell-cell communication and is coordinated through an active wave mechanism. Using a live transcriptional reporter, we show that a wave of Eda/NF-κB activity precedes scale initiation and is required for scale formation. Experiments decoupling the propagation of the wave from dermal placode formation and osteoblast differentiation demonstrate that the Eda/NF-kB activity wavefront times the sequential patterning of scales. Moreover, this decoupling resulted in defects in scale size and significant deviations in the hexagonal patterning of scales. Thus, our results demonstrate that a biochemical traveling wave coordinates scale initiation and proper hexagonal patterning across the fish body.