The equatorial eastern Indian Ocean hosts a diffuse plate boundary, where widespread deformation accommodates the relative motion between the Indian, Australian and Capricorn sub-plates. We integrate IODP Expedition 362 borehole data, which for the first time provides an accurate, ground-truthed chronostratigraphy of the sedimentary sequence east of the Ninety East Ridge (NER), with 2D seismic reflection profiles and multibeam bathymetry to assess the styles of faulting between the NER and the Sunda subduction zone, timing of activity and comparison with physical and rheological properties. We identify four distinct fault sets east of the NER in the northern Wharton Basin. N-S (350-010°) orientated faults, associated with the N-S fracture zones formed at the now extinct Wharton spreading centre, are still active and have been continuously active since at least 10 Ma. NNE- and WNW-trending fault fabrics develop between the fracture zones. The orientations and likely sense of displacement on these three sets of faults defines a Riedel shear system responding to ∼NNE-SSW left-lateral strike-slip activity at depth, demonstrated by the recent 2012 great intraplate earthquakes. We also find evidence of ∼NE-SW reverse faults, similar in style to E-W reverse faults observed west of the NER, where reverse faulting is more dominant. We show that the activity of this strike-slip system increased ca. 7-9 Ma, contemporaneous with reverse faulting and intraplate deformation west of the NER.