Purpose Fourier encoded MRI signal is complex and, therefore, sensitive to uncontrolled phase variations caused, e.g., by object motion. An alternative encoding is proposed which leads to phaseless (positive real) signals and allows the phase fluctuations to be removed by simple magnitude calculation before the Fourier transform. Theory and Methods Phaseless encoding uses harmonic modulation of the longitudinal magnetization with different frequencies and phases before excitation. It can be combined with Fourier encoding of complementary dimensions to produce, e.g., a 3D version of echo planar imaging insensitive to intershot phase variations. It can also be mixed with Fourier encoding of the same dimension allowing a high‐resolution image to be obtained from magnitude‐reconstructed low‐resolution components. The latter is a generalization of the super‐resolution MRI with microscopic tagging proposed recently. Improved reconstruction for this technique was adopted from its optical analogue, harmonic excitation light microscopy (HELM). Results Artifact free images were obtained despite phase fluctuations caused by random receiver reference and object motion during diffusion weighting. Proposed reconstruction of mixed‐encoded data reaches higher resolution than the original super‐resolution method.