The redox state of Precambrian shallow seas has been linked with material cycle and evolution of the photosynthesis-based ecosystem. Iron is a redox-sensitive element and exists as a soluble Fe(II) species or insoluble Fe(III) species on Earth’s surface. Previous studies have shown that the iron isotopic ratio of marine sedimentary minerals is useful for understanding the ocean redox state, although the redox state of the Archean shallow sea is poorly known. This is partly because the conventional bulk isotope analytical technique has often been used, wherein the iron isotopic record may be dampened by the presence of isotopically different iron-bearing minerals within the same sample. Here we report a microscale iron isotopic ratio of individual pyrite grains in shallow marine stromatolitic carbonates over geological time using a newly developed, near-infrared femtosecond laser ablation multicollector ICP-MS technique (NIR-fs-LA-MC-ICP-MS).We have determined that the grain-scale iron isotopic distribution of pyrite from coeval samples shows a bimodal (2.7 and 2.3 Ga) or unimodal pattern (2.9, 2.6, and 0.7 Ga). In particular, pyrite from the 2.7 Ga Fortescue Group shows a unique bimodal distribution with highly positive (+1.0‰ defined as Type 1) and negative δ56Fe values (−1.8‰ defined as Type 2). Type 1 and 2 pyrites occasionally occur within different siliceous layers in the same rock specimen. Layer-scale iron isotopic heterogeneity indicates that the iron isotopic ratios of the two types of pyrite are not homogenized by diagenesis after deposition. Some cubic pyrites have a core with a positive δ56Fe value (1‰) and a rim with a crustal δ56Fe value (0‰). The observed isotopic zoning suggests that the positive δ56Fe value is a primary signature at the time of stromatolite formation, while secondary pyrite precipitated during diagenesis.The positive δ56Fe value of Type 1 and the large iron isotopic difference between Type 1 and 2 (2.8‰.) suggest partial Fe(II) oxidation in the 2.7-Ga shallow sea, i.e., pyritization of 56Fe-enriched ferric oxyhydroxide (Type 1) and 56Fe depleted Fe2+aq in seawater (Type 2). Type 2 pyrite was probably not produced by microbial iron redox cycling during diagenesis because this scenario requires a higher abundance of pyrite with δ56Fe of 0‰ than of −1.8‰. Consequently, the degree of Fe(II) oxidation in the 2.7-Ga shallow sea can be estimated by a Fe2+aq steady-state model. The model calculation shows that half the Fe2+aq influx was oxidized in the seawater. This implies that O2 produced by photosynthesis would have been completely consumed by oxidation of the Fe2+aq influx. Grain-scale iron isotopic distribution of pyrite could be a useful index for reconstructing the redox state of the Archean shallow sea.