We report a ~38 ks X-ray observation of McNeils Nebula obtained with XMM on 2004 April 4. V1647 Ori, the young star in outburst illuminating McNeils Nebula, is detected with XMM and appears variable in X-rays. We investigate the hardness ratio variability and time variations of the event energy distribution with quantile analysis, and show that the large increase of the count rate from V1647 Ori observed during the second half of the observation is not associated with any large plasma temperature variations as for typical X-ray flares from young low-mass stars. X-ray spectral fitting shows that the bulk (~75%) of the intrinsic X-ray emission in the 0.5-8 keV energy band comes from a soft plasma component (0.9 keV) reminiscent of the X-ray spectrum of the classical T Tauri star TW Hya, for which X-ray emission is believed to be generated by an accretion shock onto the photosphere of a low-mass star. The hard plasma component (4.2 keV) contributes ~25% of the total X-ray emission, and can be understood only in the framework of plasma heating sustained by magnetic reconnection events. We find a hydrogen column density of NH=4.1E22 cm-2, which points out a significant excess of hydrogen column density compared to the value derived from optical/IR observations, consistent with the picture of the rise of a wind/jet unveiled from ground optical spectroscopy. The X-ray flux observed with XMM ranges from roughly the flux observed by Chandra on 2004 March 22 (~10 times greater than the pre-outburst X-ray flux) to a value two times greater than that caught by Chandra on 2004 March 7 (~200 times greater than the pre-outburst X-ray flux). We have investigated the possibility that V1647 Ori displays a periodic variation in X-ray brightness as suggested by the combined Chandra+XMM data set (abridged).