SNAREs constitute the core machinery of intracellular membrane fusion but vesicular SNAREs localize to specific compartments via largely unknown mechanisms. Here we identified an interaction between VAMP7 and SNAP-47 using a proteomics approach. We found that SNAP-47 mainly localized to cytoplasm, the endoplasmic reticulum and ERGIC and could also shuttle between the cytoplasm and the nucleus. SNAP-47 preferentially interacted with TGN VAMP4 and post-Golgi VAMPs 7 and 8. SNAP-47 also interacted with ER and Golgi Syntaxin 5 and with Syntaxin 1 in the absence of Munc18a, when Syntaxin 1 is retained in the ER. A C-terminally truncated SNAP-47 was impaired in interaction with VAMPs and affected their subcellular distribution. SNAP-47 silencing further shifted the subcellular localization of VAMP4 from the Golgi apparatus to the ER. WT and mutant SNAP-47 overexpression impaired VAMP7 exocytic activity. We conclude that SNAP-47 plays a role in the proper localization and function of a subset of VAMPs likely via regulation of their transport through the early secretory pathway.