Pyrite framboid in sedimentary rocks could be concerned with arsenic contamination in groundwater of acidic environment and has been studied for the formation process of its unique morphology. However, little has been discussed about the formation process based on heavy-metal distribution in pyrite framboids and their aggregates. To reveal the formation process of pyrite framboids and their aggregates, mudstone from the Late Cretaceous Hakobuchi Group, central Hokkaido, Japan, are investigated for mode, petrographical, mineralogical, and micro-PIXE (particle-induced x-ray emission) analysis in this study. Spherical and sub-spherical pyrite framboids observed in polyframboids can be divided into two types based on diameter of framboids (D) and the average diameter of microcrystals (d) within framboids: type 1, ranging from 2 to 9 μm and from 0.4 to 0.9 μm, respectively, and type 2, ranging from 8 to 50 μm and from 0.5 to 1.8 μm, respectively. Based on the quantitative traverse analyses and 2-D elemental mapping results by micro-PIXE, heterogeneities in the concentrations of heavy metals within the analyzed aggregations of pyrite are exhibited. On the basis of the As and Pb zoning patterns, the time range and chronological stages of pyrite-aggregation growth are revealed.