A scintillation resistant sensor that allows retrieval of an input optical wave phase using a multi-aperture phase reconstruction (MAPR) technique is introduced and analyzed. The MAPR sensor is based on a low-resolution lenslet array in the classical Shack–Hartmann arrangement and two high-resolution photo-arrays for simultaneous measurements of pupil- and focal-plane intensity distributions, which are used for retrieval of the wavefront phase in a two stage process: (a) phase reconstruction inside the sensor pupil subregions corresponding to lenslet subapertures and (b) recovery of subaperture averaged phase components (piston phases). Numerical simulations demonstrate the efficiency of the MAPR technique in conditions of strong intensity scintillations and the presence of wavefront branch points.