Random numbers are required for a variety of applications from secure communications to Monte-Carlo simulation. Yet randomness is an asymptotic property and no output string generated by a physical device can be strictly proven to be random. We report an experimental realization of a quantum random number generator (QRNG) with randomness certified by quantum contextuality and the Kochen-Specker theorem. The certification is not performed in a device-independent way but through a rigorous theoretical proof of each outcome being value-indefinite even in the presence of experimental imperfections. The analysis of the generated data confirms the incomputable nature of our QRNG.