At birth, synaptic sites in developing rodent muscles are innervated by numerous motor axons. During subsequent weeks, this multiple innervation disappears as one terminal strengthens, and all the others are eliminated. Experimental perturbations that alter neuromuscular activity affect the rate of synaptic refinement, with more activity accelerating the time to single innervation and neuromuscular blockade retarding it. However, it remains unclear whether patterns of muscle use (driven by endogenous neuronal activity) contribute to the rate of synapse elimination. For this reason we examined the timing of supernumerary nerve terminal elimination at synapses in extraocular muscles (EOMs), a specialized set of muscles controlling eye movements. On the basis of their exceptionally high patterns of activity, we hypothesized that synaptic refinement would be greatly accelerated at these synapses. We found, however, that rates of synaptic refinement were only modestly accelerated in rectus and oblique EOMs compared with synapses in somite-derived skeletal muscle. In contrast to these results, we observed a dramatic delay in the elimination of supernumerary nerve terminals from synapses in the levator palpebrae superioris (LPS) muscle, a specialized EOM that initiates and maintains eyelid elevation. In mice, natural eye opening occurs at the end of the second postnatal week of development. Thus, although synapse elimination is occurring in most EOMs and somite-derived skeletal muscles, it appears to be dramatically delayed in a set of specialized eyelid muscles that remain immobile during early postnatal development.