BACE1, a major therapeutic target for treatment of Alzheimer's disease, functions within a narrow pH range. Despite tremendous effort and progress in the development of BACE1 inhibitors, details of the underlying pH-dependent regulatory mechanism remain unclear. Here we elucidate the pH-dependent conformational mechanism that regulates BACE1 activity using continuous constant-pH molecular dynamics (MD). The simulations reveal that BACE1 mainly occupies three conformational states and that the relative populations of the states shift according to pH. At intermediate pH, when the catalytic dyad is monoprotonated, a binding-competent state is highly populated, while at low and high pH a Tyr-inhibited state is dominant. Our data provide strong evidence supporting conformational selection as a major mechanism for substrate and peptide-inhibitor binding. These new insights, while consistent with experiment, greatly extend the knowledge of BACE1 and have implications for further optimization of inhibitors and understanding potential side effects of targeting BACE1. Finally, the work highlights the importance of properly modeling protonation states in MD simulations.