We investigated changes in two gonadotropin releasing hormone (GnRH)-containing neuronal populations during juvenile development in the African teleost, Haplochromis burtoni. Juveniles were sampled at weekly intervals and GnRHir neurons were identified through immunocytochemistry (ICC), then counted and measured on computer-captured video images. Soma size of GnRH neurons in the preoptic area (POA), which regulate gonadotropin release from the pituitary, is socially modulated in adults. Here we show that in juveniles the soma size of these neurons increases as a linear function of body weight. Terminal nerve (TN) GnRHir neurons, in contrast, are not involved in pituitary regulation and their soma size is not socially modulated in adults. In juveniles, soma size of these neurons is a quadratic function of body size and the covariance of soma size and body size is much less than in the POA GnRHir neurons. In both populations, GnRHir neuronal number covaries with body size or age only in the earliest juvenile stages. Analysis of the development of these two distinct GnRHir neuronal populations provides insight into their functional differentiation in adults.