Fragile X syndrome (FXS), the most common inherited intellectual disability and monogenic cause of autism, results from loss of FMRP, which regulates mRNA translation essential for brain development and synaptic plasticity. FMRP has been implicated in the synaptic localization and surface expression of various membrane proteins, yet underlying mechanisms remain unclear. Here, we identified a broad dysregulation of membrane surface and associated proteins in FMRP-deficient neurons by quantitative mass spectrometry. Among them, we found increased steady-state levels of several subunits of the clathrin-adaptor protein complex 2 (AP-2), including AP2A1 and AP2B1.