The presence and conservation of GnRH2 across vertebrate species suggest important biological roles. However, the function of GnRH2 remains unclear. A good research model for GnRH2 functional studies is still lacking largely due to the absence of GnRH2 in the widely used mouse model. Hence, we used the zebrafish, for which powerful genetic tools are available, and developed a transgenic (Tg) line expressing enhanced green fluorescence protein (eGFP). The high sensitivity of eGFP, which can diffuse throughout the neuron, enables us to document the complete projectome of GnRH2 neurons at different developmental stages. Fine projection structures were observed without sacrificing the fish. Crossed with the GnRH3:tdTomato Tg line, the GnRH2:eGFP Tg line provides us with an opportunity to visualize the entire GnRH system simultaneously in one organism. This work will provide a framework to understand the function of the highly-conserved GnRH2 system.