Background Indigenous fire management in northern Australian savannas (beginning at least 11,000 years ago) involved frequent, small, cool, early dry season fires. This fire regime changed after European arrival in the late 1700s to unmanaged fires that burn larger areas, late in the dry season, detrimental to carbon stocks and biodiversity. Aims Test the hypothesis that significant sequestration of pyrogenic carbon in soil accompanies the reimposition of an Indigenous fire regime. Methods Savanna soils under the same vegetation, but with the number of fires varying from 0 to 13 (irrespective of the season) between 2000 and 2022 were sampled. Organic and pyrogenic carbon stocks as well as carbon isotope composition of the 0–5 cm soil layer were determined along sample transects with varying fire return intervals. Key results An average increase of 0.25 MgC ha−1 was observed in soil pyrogenic carbon stocks in transects with ≥5 fires, compared to transects with 0–4 fires, with a small increase in soil organic carbon stocks that was not significant. Conclusions A return to more frequent fires early in the dry season has the potential to sequester significant pyrogenic carbon in northern Australian savanna soils on decadal timescales.