The structure of nano-crystalline $MnFe_2O_4$ was determined and refined with electron powder diffraction data employing the Rietveld refinement technique. A nano-crystalline sample (with average crystal size of about 10.9 nm) was characterized by selected area electron diffraction in an energy-filtering transmission electron microscope operated at 120 kV. All reflection intensities were extracted from a digitized image plate using the program ELD and then used in the course of structure refinements employing the program FULLPROF for the Rietveld analysis. The final structure was refined in space group Fd-3m (# 227) with lattice parameters a=8.3413(7) $AA$. The reliability factors of the refinement are $R_F$=7.98% and $R_B$=3.55%. Comparison of crystallographic data between electron powder diffraction data and reference data resulted in better agreement with ICSD-56121 rather than with ICSD-28517 which assumes an initial structure model.