We report that hemozoin nanocrystals demonstrate superparamagnetic properties, with direct measurements of the synthetic hemozoin magnetization. The results show that the magnetic permeability constant varies from μ = 4585 (at −20 °C) to 3843 (+20 °C), with the values corresponding to a superparamagnetic system. Similar results were obtained from the analysis of the diffusion separation of natural hemozoin nanocrystals in the magnetic field gradient, with μ = 6783 exceeding the value obtained in direct measurements by the factor of 1.8. This difference is interpreted in terms of structural differences between the synthetic and natural hemozoin. The ab initio analysis of the hemozoin elementary cell showed that the Fe3+ ion is in the high-spin state (S = 5/2), while the exchange interaction between Fe3+ electron-spin states was much stronger than kBT at room temperature. Thus, the spin dynamics of the neighboring Fe3+ ions are strongly correlated, lending support to the superparamagnetism.