AbstractQuantum logic gates are backbones of quantum information processing (QIP), wherein the typical three-qubit Fredkin and Toffoli gates are essential in quantum computation and communication. So far, the quantum Fredkin gate has only been demonstrated with pre-entangled input states in free-space optics, which limits its usage for independent input photons. Here, we put forward an exquisite scheme and experimentally perform a proof-of-principle demonstration of three-qubit Fredkin and Toffoli gates on a programmable quantum photonic chip. Our scheme can also be used to realize a series of other two-qubit quantum gates. Our work sheds light on the merits of quantum photonic chip in implementing quantum logic gates, and paves the way for advanced quantum chip processors.