Highly polarized cells such as photoreceptors require precise and efficient strategies for establishing and maintaining the proper subcellular distribution of proteins. The signals and molecular machinery that regulate trafficking and sorting of synaptic proteins within cone inner segments is mostly unknown. In this study, we show that the polyphosphoinositide phosphatase Synaptojanin 1 (SynJ1) is critical for this process. We used transgenic markers for trafficking pathways, electron microscopy, and immunocytochemistry to characterize trafficking defects in cones of the zebrafish mutant, nrca14, which is deficient in phosphoinositide phosphatase, SynJ1. The outer segments and connecting cilia of nrca14 cone photoreceptors are normal, but RibeyeB and VAMP2/synaptobrevin, which normally localize to the synapse, accumulate in the nrca14 inner segment. The structure of the Endoplasmic Reticulum in nrca14 mutant cones is normal. Golgi develop normally, but later become disordered. Large vesicular structures accumulate within nrca14 cone photoreceptor inner segments, particularly after prolonged incubation in darkness. Cone inner segments of nrc a14 mutants also have enlarged acidic vesicles, abnormal late endosomes, and a disruption in autophagy. This last pathway also appears exacerbated by darkness. Taken altogether, these findings show that SynJ1 is required in cones for normal endolysosomal trafficking of synaptic proteins.