We present a geochemical dataset and cathodoluminescence images of apatite from the Neoarchean (2610 Ma) glimmerite-carbonatite rocks from the Siilinjärvi complex, Eastern Finland. The subhedral, tapered prismatic grains are compositionally fluorapatite, with limited substitution of Ca by Sr, Na and low REE and Si contents. The Sr/Y ratios are among the highest in a global apatite comparison, comparable to those from other calcite carbonatites, dolomite carbonatites, and phoscorites. Some grains show evidence of late- or post-magmatic interaction with a carbonatite magma or a hydrothermal fluid, resulting in REE-rich overgrowth rims or recrystallized grains with abundant fluid inclusions. We interpret the high Sr/Y ratios combined with low REE contents and depleted heavy REE+Y to represent crystallization from a mantle-derived carbonatite parental magma. We show that the Siilinjärvi apatite is chemically heterogeneous but with a limited range in compositions. There are noticeable compositional differences on all spatial scales from micrometer to tens of meters, i.e., within a single crystal, between crystals in a sample, between samples and the two individual sampling locations. We conclude that the intra-crystal geochemical variability in apatite is a suitable tracer of the magmatic and post-magmatic evolution of carbonatite complexes.