The ~150 km wide dextral Marlborough Fault System and adjacent Kaikoura Mountains accommodate oblique convergence at the NE end of the South Island, New Zealand. Low-temperature thermochronology from this region, which was also the site of the 2016 Mw7.8 Kaikoura earthquake, places new limits on the timing and style of mountain building and the relationship between the mountains and adjacent faults. We sampled rocks for (U-Th/He) and fission track dating from a range of elevations spanning ~2 km within the Kaikoura Mountains, which stand high above active strike-slip faults. The data reveal two phases of exhumation: Miocene cooling localized to hanging wall rocks followed by regional and rapid cooling reflected in all samples starting at ~4-5 Ma. These results suggest that, despite the presence of active mountain front faults, much of the topographic relief in this region predates the onset of strike-slip faulting when portions of the Marlborough Faults were thrust faults during the early development of the transpressive plate boundary. After 5 Ma, the main Marlborough faults transitioned to accommodating primarily strike-slip motion, and regional exhumation likely reflected increased proximity to the migrating Pacific plate subduction zone and the buoyant Chatham Rise. The 2016 earthquake, which lifted and/or laterally shifted the surface along multiple subsidiary Marlborough fault strands, both onshore and off, fits well with evidence from the long-term record of a broad, complex and evolving oblique collision zone.