We present a galaxy cluster survey based on XMM-Newton observations that are located in Stripe 82 of the Sloan Digital Sky Survey (SDSS). The survey covers an area of 11.25 deg2. The X-ray cluster candidates were selected as serendipitously extended detected sources from the third XMM-Newton serendipitous source catalogue (3XMM-DR5). A cross-correlation of the candidate list that comprises 94 objects with recently published X-ray and optically selected cluster catalogues provided optical confirmations and redshift estimates for about half of the candidate sample. We present a catalogue of X-ray cluster candidates previously known in X-ray and/or optical bands from the matched catalogues or NED. The catalogue consists of 54 systems with redshift measurements in the range of 0.05–1.19 with a median of 0.36. Of these, 45 clusters have spectroscopic confirmations as stated in the matched catalogues. We spectroscopically confirmed another 6 clusters from the available spectroscopic redshifts in the SDSS-DR12. The cluster catalogue includes 17 newly X-ray discovered clusters, while the remainder were detected in previous XMM-Newton and/or ROSAT cluster surveys. Based on the available redshifts and fluxes given in the 3XMM-DR5 catalogue, we estimated the X-ray luminosities and masses for the cluster sample. We also present the list of the remaining X-ray cluster candidates (40 objects) that have no redshift information yet in the literature. Of these candidates, 25 sources are considered as distant cluster candidates beyond a redshift of 0.6. We also searched for galaxy cluster mergers in our cluster sample and found two strong candidates for newly discovered cluster mergers at redshifts of 0.11 and 0.26. The X-ray and optical properties of these systems are presented.