Puerto Rico and the northern Virgin Islands together preserve a unique archive of island arc construction and plate margin deformation along the northeastern edge of the Caribbean plate. In Eocene times, arc-continent collision of the Caribbean plate and the North American plate led to transpressional deformation along two major fault systems in Puerto Rico, resulting in an island-wide depositional hiatus. Although styles and kinematics of this deformational event are seemingly well understood, the lack of chronologic constraints have left uncertainties related to the timing of inception and activity, the magnitude of crustal exhumation, and the character of deformation (i.e., progressive or polyphase). New zircon and apatite (U-Th)/He ages reveal that deformation associated with arc-continent collision started in the early Eocene (ca. 52 Ma) and ended in the early Oligocene (ca. 29 Ma). Over this 23 m.y. time frame, deformation was not restricted to major faults, instead it propagated gradually eastward, with punctuated episodes of vertical exhumation in the early Eocene (ca. 52–34 Ma) and late Eocene (ca. 36–29 Ma). In contrast, the northern Virgin Islands experienced rapid cooling and exhumation in the early Miocene (ca. 24–21 Ma) associated with the extensional opening of the Anegada Passage. The modeled thermal histories for the central and northeastern part of Puerto Rico indicate collision-related peak transpressional deformation between 36 and 29 Ma and an average exhumation rate 0.9 ± 0.6 km/m.y. These results represent the first direct constraints on the timing and magnitude of collisional exhumation and offer insights into the deformational evolution of the northeastern edge of the Caribbean plate.