In light of the escalating demand for computing powers, wave‐based analog computers have emerged as a compelling study area due to their remarkable capacity for ultra‐fast operation. Here, a programmable wave‐based computer, based on programmable meta‐structures is proposed, which is also called as meta‐computer. The meta‐computer can perform various types of analog computations in real‐time in the electromagnetic (EM) wave space, including matrix‐vector multiplication, discrete Fourier transform, filtering, and solving complex matrix equations. Owing to the powerful capability of the programmable meta‐structures in manipulating the EM fields and waves in real‐time, the proposed meta‐computer exhibits the advantages of flexible re‐programmability, low complexity, and direct computation in the EM space. Two prototypes of the meta‐computer in the microwave frequency are designed and fabricated, and the computing capability is validated through both numerical simulations and experiments. This work contributes a prominent approach for fully programmable wave‐based computers with noteworthy implications for expanding the applications of analog computing.