Conventional quantum key distribution (QKD) typically uses binary encoding based on photon polarization or time-bin degrees of freedom and achieves a key capacity of at most one bit per photon. Under photon-starved conditions the rate of detection events is much lower than the photon generation rate, because of losses in long distance propagation and the relatively long recovery times of available single-photon detectors. Multi-bit encoding in the photon arrival times can be beneficial in such photon-starved situations. Recent security proofs indicate high-dimensional encoding in the photon arrival times is robust and can be implemented to yield high secure throughput. In this work we demonstrate entanglement-based QKD with high-dimensional encoding whose security against collective Gaussian attacks is provided by a high-visibility Franson interferometer. We achieve unprecedented key capacity and throughput for an entanglement-based QKD system because of four principal factors: Franson interferometry that does not degrade with loss; error correction coding that can tolerate high error rates; optimized time–energy entanglement generation; and highly efficient WSi superconducting nanowire single-photon detectors. The secure key capacity yields as much as 8.7 bits per coincidence. When optimized for throughput we observe a secure key rate of 2.7 Mbit s−1 after 20 km fiber transmission with a key capacity of 6.9 bits per photon coincidence. Our results demonstrate a viable approach to high-rate QKD using practical photonic entanglement and single-photon detection technologies.