Guanine nucleotide exchange is essential for Rab GTPase activities in regulating intracellular vesicle trafficking. This exchange process is facilitated by guanine nucleotide exchange factor (GEF). Previously, we identified Caenorhabditis elegans AEX-3 as a GEF for Rab3 GTPase. Here we demonstrate that AEX-3 regulates neural activities through a second, previously unrecognized pathway via interactions with the novel protein CAB-1. CAB-1 is 425 amino acids long and has an 80 amino acid motif in common with the mouse neural protein NPDC-1. cab-1 and rab-3 mutants have different behavioral defects, and RAB-3 localization and function are apparently normal in cab-1 mutants, indicating that the CAB-1 pathway is distinct from the RAB-3 pathway. The aex-3 mutant phenotype resembles the sum of the rab-3 and cab-1 mutant phenotypes, indicating that AEX-3 regulates two different pathways for neural activities. We propose that connection of multiple pathways may be an important feature of Rab GEFs to coordinate various cellular events.