Two conceptually related variable‐flip‐angle 3D spin‐echo pulse sequences were designed for imaging at voxel sizes of 2–5 × 10⁻³ mm³ corresponding to pixel areas of less than 100 × 100 μm² and section thicknesses on the order of 300–400 μm on a conventional 1.5 T MR imaging system equipped with 1 G/cm imaging field gradients, providing 12 sections in 10 min imaging time. The pulse sequences make use of the concept of restoring longitudinal magnetization inverted by the 180° phase reversal pulse and are derivatives of pulse sequences previously dubbed “FATE” and “RASEE.” It is shown that even in the small‐voxel regime (< 10⁻² mm³ voxel size) and at echo times on the order of 10 ms, gradient echo images are sensitive to intrinsic fields causing artifactual boundary effects, including signal loss from intravoxel phase scrambling and spatial mismapping. At this resolution the variable flipangle spin‐echo pulse sequences are demonstrated to be better suited for imaging magnetically heterogeneous systems such as trabecular bone microstructure in vivo. These pulse sequences are found to be substantially less sensitive to distortions from magnetic dipole fields occurring at the boundaries of two phases of different magnetic permeability.