Most work in quantum circuit optimization has been performed in isolation from the results of quantum fault-tolerance. Here we present a polynomial-time algorithm for optimizing quantum circuits that takes the actual implementation of fault-tolerant logical gates into consideration. Our algorithm resynthesizes quantum circuits composed of Clifford group and T gates, the latter being typically the most costly gate in fault-tolerant models, e.g., those based on the Steane or surface codes, with the purpose of minimizing both T-count and T-depth. A major feature of the algorithm is the ability to resynthesize circuits with ancillae at effectively no additional cost, allowing space-time trade-offs to be easily explored. The tested benchmarks show up to 65.7% reduction in T-count and up to 87.6% reduction in T-depth without ancillae, or 99.7% reduction in T-depth using ancillae.