This paper deals with the estimation of spectral acceleration for Manipur based on probabilistic seismic hazard analysis (PSHA). The 500 km region surrounding Manipur is divided into seven tectonic zones and major faults located in these zones are used to estimate seismic hazard. The earthquake recurrence relations for the seven zones have been estimated from past seismicity data. Ground motion prediction equations proposed by Boore and Atkinson (2008 Earthq. Spectra24 99–138) for shallow active regions and Atkinson and Boore (2003 Bull. Seismol. Soc. Am.93 1703–29) for the Indo-Burma subduction zone are used for estimating ground motion. The uniform hazard response spectra for all the nine constituent districts of Manipur (Senapati, Tamenglong, Churachandpur, Chandel, Imphal east, Imphal west, Ukhrul, Thoubal and Bishnupur) at 100-, 500- and 2500-year return periods have been computed from PSHA. A contour map of peak ground acceleration over Manipur is also presented for 100-, 500-, and 2500-year return periods with variations of 0.075–0.225, 0.18–0.63 and 0.3–0.1.15 g, respectively, throughout the state. These results may be of use to planners and engineers for site selection, designing earthquake resistant structures and, further, may help the state administration in seismic hazard mitigation.