Astronomers have found more than a dozen planets transiting stars that are 10–40 million years old1, but younger transiting planets have remained elusive. The lack of such discoveries may be because planets have not fully formed at this age or because our view is blocked by the protoplanetary disk. However, we now know that many outer disks are warped or broken2; provided the inner disk is depleted, transiting planets may thus be visible. Here we report observations of the transiting planet IRAS 04125+2902 b orbiting a 3-million-year-old, 0.7-solar-mass, pre-main-sequence star in the Taurus Molecular Cloud. The host star harbours a nearly face-on (30 degrees inclination) transitional disk3 and a wide binary companion. The planet has a period of 8.83 days, a radius of 10.7 Earth radii (0.96 Jupiter radii) and a 95%-confidence upper limit on its mass of 90 Earth masses (0.3 Jupiter masses) from radial-velocity measurements, making it a possible precursor of the super-Earths and sub-Neptunes frequently found around main-sequence stars. The rotational broadening of the star and the orbit of the wide (4 arcseconds, 635 astronomical units) companion are both consistent with edge-on orientations. Thus, all components of the system are consistent with alignment except the outer disk; the origin of this misalignment is unclear.