Quantum systems, in general, output data that cannot be simulated efficiently by a classical computer, and hence is useful for solving certain mathematical problems and simulating quantum many-body systems. This also implies, unfortunately, that verification of the output of the quantum systems is not so trivial, since predicting the output is exponentially hard. As another problem, quantum system is very delicate for noise and thus needs error correction. Here we propose a framework for verification of the output of fault-tolerant quantum computation in the measurementbased model. Contrast to existing analyses on fault-tolerance, we do not assume any noise model on the resource state, but an arbitrary resource state is tested by using only single-qubit measurements to verify whether the output of measurement-based quantum computation on it is correct or not. The overhead for verification including classical processing is linear in the size of quantum computation. Since full characterization of quantum noise is exponentially hard for large-scale quantum computing systems, our framework provides an efficient way of practical verification of experimental quantum error correction. Moreover, the proposed verification scheme is also compatible to measurement-only blind quantum computation, where a client can accept the delegated quantum computation even when a quantum sever makes deviation, as long as the output is correct.