The sorting of signaling receptors into and out of cilia relies on the BBSome, a complex of Bardet-Biedl syndrome (BBS) proteins, and on the intraflagellar transport (IFT) machinery. GTP loading onto the Arf-like GTPase ARL6/BBS3 drives assembly of a membrane-apposed BBSome coat that promotes cargo entry into cilia, yet how and where ARL6 is activated remains elusive. Here, we show that the Rab-like GTPase IFT27/RABL4, a known component of IFT complex B, promotes the exit of BBSome and associated cargoes from cilia. Unbiased proteomics and biochemical reconstitution assays show that, upon disengagement from the rest of IFT-B, IFT27 directly interacts with the nucleotide-free form of ARL6. Furthermore, IFT27 prevents aggregation of nucleotide-free ARL6 in solution. Thus, we propose that IFT27 separates from IFT-B inside cilia to promote ARL6 activation, BBSome coat assembly, and subsequent ciliary exit, mirroring the process by which BBSome mediates cargo entry into cilia. Display omitted •The IFT-B subunit IFT27/RabL4 directly and selectively binds nucleotide-empty ARL6•IFT27 needs disengagement from IFT-B to recognize ARL6•The exit of BBSome and cargoes from cilia requires IFT27•The BBSome dissociates from IFT trains in the absence of IFT27 The Arf-like GTPase ARL6 triggers BBSome coat assembly and cargo entry into cilia. Now, Liew et al. find that the Rab-like GTPase IFT27 disengages from anterograde IFT complexes to bind and activate nucleotide-empty ARL6 and thereby promote the exit of the BBSome and its associated cargoes from cilia.