Realizing universal fault-tolerant quantum computation is a key goal in quantum information science1–4. By encoding quantum information into logical qubits using quantum error correcting codes, physical errors can be detected and corrected, enabling a substantial reduction in logical error rates5–11. However, the set of logical operations that can be easily implemented on these encoded qubits is often constrained1,12, necessitating the use of special resource states known as ‘magic states’13 to implement universal, classically hard circuits14. A key method to prepare high-fidelity magic states is to perform ‘distillation’, creating them from multiple lower-fidelity inputs13,15. Here we present the experimental realization of magic state distillation with logical qubits on a neutral-atom quantum computer. Our approach uses a dynamically reconfigurable architecture8,16 to encode and perform quantum operations on many logical qubits in parallel. We demonstrate the distillation of magic states encoded in d = 3 and d = 5 colour codes, observing improvements in the logical fidelity of the output magic states compared with the input logical magic states. These experiments demonstrate a key building block of universal fault-tolerant quantum computation and represent an important step towards large-scale logical quantum processors.
