Motor neurons, skeletal muscles, and perisynaptic Schwann cells interact with extracellular matrix (ECM) to form the tetrapartite synapse in the peripheral nervous system. Dynamic remodeling of ECM composition is essential to diversify its functions for distinct cellular processes during neuromuscular junction (NMJ) development. In this review, we give an overview of the proteolytic regulation of ECM proteins, particularly by secreted and membrane-type matrix metalloproteinases (MMPs), in axonal growth and NMJ development. It is suggested that MMP-2, MMP-9, and membrane type 1-MMP (MT1-MMP) promote axonal outgrowth and regeneration upon injury by clearing the glial scars at the lesion site. In addition, these MMPs also play roles in neuromuscular synaptogenesis, ranging from spontaneous formation of synaptic specializations to activity-dependent synaptic elimination, via proteolytic cleavage or degradation of growth factors, neurotrophic factors, and ECM molecules. For instance, secreted MMP-3 has been known to cleave agrin, the main postsynaptic differentiation inducer, further highlighting the importance of MMPs in NMJ formation and maintenance. Furthermore, the increased level of several MMPs in myasthenia gravis (MG) patient suggest the pathophysiological mechanisms of MMP-mediated proteolytic degradation in MG pathogenesis. Finally, we speculate on potential major future directions for studying the regulatory functions of MMP-mediated ECM remodeling in axonal growth and NMJ development.