Magnetic field aligned freeze casting is a novel method to fabricate porous, anisotropic ceramic scaffolds with a hierarchy of architectural alignment in multiple directions. A weak rotating magnetic field applied normal to the ice growth direction in a uniaxial freezing apparatus allowed the manipulation of magnetic nanoparticles to create different pore structures and channels with long-range order in directions parallel and perpendicular to the freezing direction. Porous scaffolds consisting of different host ceramics (hydroxyapatite (HA), ZrO2, Al2O3, or TiO2) mixed with varying concentrations (0–9wt%) of Fe3O4 nanoparticles were fabricated by freeze casting under three different conditions: (1) no magnetic field, (2) a static magnetic field of 0.12T, or (3) a rotating magnetic field of 0.12T at 0.05rpm. The HA, ZrO2, and Al2O3 scaffolds showed biphasic material properties with separate Fe3O4-rich and Fe3O4-poor regions. The TiO2 scaffolds showed homogeneous distributions of Fe3O4 throughout the macrostructures, which resulted in aligned pore channels parallel to the magnetic field, normal to the ice growth direction. In the magnetic field direction, the compressive strength and stiffness of the TiO2 scaffolds containing Fe3O4 was doubled. The enhanced mechanical performance of the field aligned TiO2 scaffolds are the result of the long-range microstructural order in multiple directions—(1) the magnetic field direction and (2) the ice growth direction.