We study coherent quantum phase-slips in a Josephson junction chain, including two types of quenched disorder: random spatial modulation of the junction areas and random induced background charges. Usually, the quantum phase-slip amplitude is sensitive to the normal mode structure of superconducting phase oscillations in the ring (Mooij-Schon modes, which are all localized by the area disorder). However, we show that the modes contribution to the disorder-induced phase-slip action fluctuations is small, and the fluctuations of the action on different junctions are mainly determined by the local junction parameters. We study the statistics of the total QPS amplitude on the chain and show that it can be non-Gaussian for not sufficiently long chains.