Palynology of exhumed Pliocene marine turbidites and marl beds on the island of Timor provide insights into crustal deformation in the Indonesian region. Between ca. 4.5 and ca. 3 Ma, palynomorphs were sourced primarily from Australia and New Guinea, with increasing swamp and mangrove elements sourced from an emerging proto-Timor. Following ca. 3.1 Ma, pollen and charcoal evidence track the rapid uplift of Timor to a high island, with the progressive appearance of montane and dry, lee-side floristic elements. Early- to mid-Pliocene uplift rates of 0.5–0.6 mm yr−1 increased to 2–5 mm yr−1 in the latest Pliocene. The rapid topographic development of Timor-Leste initiated earlier but followed a pattern similar to that of more westerly localities in the Timor sector of the Banda Arc. Timor’s emergence from the marine environment is closely correlated with the timing of closure of the Indonesian seaway to deep-dwelling foraminfera.