The regulation of RNA is crucial for spatiotemporal control of gene expression in neurons, but how the correct localization, levels, and function of synaptic proteins are achieved is not well understood. In this study, we globally investigate the role of alternative 3'UTRs in regulating RNA localization in the synaptic regions of the Drosophila brain. We identify direct mRNA targets of the translational repressor Pumilio, finding that mRNAs bound by Pumilio encode proteins enriched in synaptosomes. Pumilio differentially binds to RNA isoforms of the same gene, where shorter 3'UTRs tend to localize to the synapse, and longer 3'UTRs remain in the neuronal soma. Disruptions in 3'UTR isoform localization and axon outgrowth occur in pumilio mutant neurons. Our results reveal a mechanism of isoform-dependent protein function, demonstrating how neurons can achieve high protein complexity with a restricted set of genes. Overall design: This study assesses 3' mRNA-sequencing and proteomic raw data of D. melanogaster "Synaptosome" fractions, in addition to Pumilio 3'xRIPseq data of D. melanogaster head isolates, to assess the role of Pumilio in the localization of mRNAs, and translation of Pumilio asociated proteins at the synapse. Input controls samples were obtained for all three data sources.