PurposeThe existing approach of Nyquist ghost correction by parallel imaging in echo planar imaging (EPI) can suffer from image noise amplification. We propose a method that estimates a phase error map from multi‐channel data itself and incorporates it into the sensitivity encoding (SENSE) reconstruction for Nyquist ghost correction without compromising the image SNR.MethodsThis method first reconstructs two ghost‐free images from positive and negative echoes using SENSE, respectively, from which the phase error map is computed. This map is then incorporated into the coil sensitivity maps for the negative echo image during the joint SENSE reconstruction of all k‐space data to obtain the final ghost‐free image. Phantom and in vivo EPI experiments at 7 T and 3 T were performed to evaluate the proposed method.ResultsNyquist ghost was effectively removed in all images even under oblique imaging and poor eddy current conditions. Resulting image signal‐to‐noise ratio (SNR) was comparable to that by the traditional linear phase error correction method and higher than that by a previous SENSE‐based parallel imaging correction approach.ConclusionThe proposed correction method can robustly eliminate Nyquist ghost while preserving the image SNR. This approach requires no additional calibration data beyond standard coil sensitivity maps and can be readily applied to all EPI applications. Magn Reson Med 79:943–951, 2018. © 2017 International Society for Magnetic Resonance in Medicine.