Parkinson's disease (PD) and Alzheimer's disease (AD), two of the most common neurodegenerative diseases, are caused by both genetic and environmental factors. Mammalian neuronal cells abundantly express a deubiquitinating (DUB) enzyme, Ubiquitin Carboxy-terminal hydrolase L1 (UCH-L1), which is involved in the pathogenesis of both of these neurodegenerative diseases. This DUB is selectively expressed in the brain and its activity is required for normal synaptic function. Here we show that UCH-L1 activity is up-regulated by NMDA receptor activation and that this upregulation leads to increase in mono-Ub levels in the cell. Furthermore, we show that pharmacological inhibition of UCH-L1 leads to reduction of mono-Ub levels in the cell and causes dramatic alterations in size and distribution of many pre- and post- synaptic proteins. Moreover, for the first time we show that, both in vitro and in vivo, application of UCH-L1 specific inhibitor LDN, reduces UCH-L1 ability to bind to ubiquitin. In addition to using pharmacology, genetic tools such as RNAi against UCH-L1 and overexpression of mutant constructs were used to study the effect of altered UCH-L1 activity on synaptic protein composition. These findings suggest that through modulating mono-ubiquitin levels in cells, in an activity dependent manner, UCH-L1 plays an important role in neuronal synaptic remodeling.