Megathrust splay fault systems in accretionary prisms have been identified as conduits for long-term plate motion and significant coseismic slip during subduction earthquakes. These fault systems are important because of their role in generating tsunamis, but rarely are emergent above sea level where their long-term (million year) history can be studied. We present 32 apatite (U-Th)/He (AHe) and 27 apatite fission-track (AFT) ages from rocks along an emergent megathrust splay fault system in the Prince William Sound region of Alaska above the shallowly subducting Yakutat microplate. The data show focused exhumation along the Patton Bay megathrust splay fault system since 3–2 Ma. Most AHe ages are younger than 5 Ma; some are as young as 1.1 Ma. AHe ages are youngest at the southwest end of Montague Island, where maximum fault displacement occurred on the Hanning Bay and Patton Bay faults and the highest shoreline uplift occurred during the 1964 earthquake. AFT ages range from ca. 20 to 5 Ma. Age changes across the Montague Strait fault, north of Montague Island, suggest that this fault may be a major structural boundary that acts as backstop to deformation and may be the westward mechanical continuation of the Bagley fault system backstop in the Saint Elias orogen. The regional pattern of ages and corresponding cooling and exhumation rates indicate that the Montague and Hinchinbrook Island splay faults, though separated by only a few kilometers, accommodate kilometer-scale exhumation above a shallowly subducting plate at million year time scales. This long-term pattern of exhumation also reflects short-term seismogenic uplift patterns formed during the 1964 earthquake. The increase in rock uplift and exhumation rate ca. 3–2 Ma is coincident with increased glacial erosion that, in combination with the fault-bounded, narrow width of the islands, has limited topographic development. Increased exhumation starting ca. 3–2 Ma is interpreted to be due to rock uplift caused by increased underplating of sediments derived from the Saint Elias orogen, which was being rapidly eroded at that time.