Aim Experimental animals, such as non-human primates (NHPs), mice, Zebrafish, and Drosophila, are frequently employed as models to gain insights into human physiology and pathology. In developmental neuroscience and related research fields, information about the similarities of developmental gene expression patterns between animal models and humans is vital to choose what animal models to employ. Here, we aimed to statistically compare the similarities of developmental changes of gene expression patterns in the brains of humans with those of animal models frequently used in the neuroscience field. Methods The developmental gene expression datasets that we analyzed consist of the fold-changes and P values of gene expression in the brains of animals of various ages compared with those of the youngest postnatal animals available in the dataset. By employing the running Fisher algorithm in a bioinformatics platform, BaseSpace, we assessed similarities between the developmental changes of gene expression patterns in the human ( Homo sapiens ) hippocampus with those in the dentate gyrus (DG) of the rhesus monkey ( Macaca mulatta ), the DG of the mouse ( Mus musculus ), the whole brain of Zebrafish ( Danio rerio ), and the whole brain of Drosophila ( D. melanogaster ). Results Among all possible comparisons of different ages and animals in developmental changes in gene expression patterns within the datasets, those between rhesus monkeys and mice were highly similar to those of humans with significant overlap P -value as assessed by the running Fisher algorithm. There was the highest degree of gene expression similarity between 40–59-year-old humans and 6–12-year-old rhesus monkeys (overlap P -value = 2.1 × 10− 72). The gene expression similarity between 20–39-year-old humans and 29-day-old mice was also significant (overlap P = 1.1 × 10− 44). Moreover, there was a similarity in developmental changes of gene expression patterns between 1–2-year-old Zebrafish and 40–59-year-old humans (Overlap P-value = 1.4 × 10− 6). The overlap P -value of developmental gene expression patterns between Drosophila and humans failed to reach significance (30 days Drosophila and 6–11-year-old humans; overlap P -value = 0.0614). Conclusions These results indicate that the developmental gene expression changes in the brains of the rhesus monkey, mouse, and Zebrafish recapitulate, to a certain degree, those in humans. Our findings support the idea that these animal models are a valid tool for investigating the development of the brain in neurophysiological and neuropsychiatric studies. Supplementary Information The online version contains supplementary material available at 10.1186/s13041-021-00840-4.