The analysis of pyrogenic carbon (PyC) in environmental samples is of great interest, e.g. for carbon cycle assessment, (bio-)char characterization and palaeo-environmental or archeological reconstruction. Here, an HPLC method (HPLC) is presented that reproducibly quantifies benzene polycarboxylic acids (BPCA) as molecular markers for PyC in various kinds of environmental samples. It operates at low pH without requiring an organic modifier and was thoroughly tested with PyC reference materials and a peatland core that served as a feasibility and plausibility check. Compared to the established gas chromatography (GC) method, the HPLC method results in higher BPCA quantification reproducibility by showing a significantly smaller coefficient of variation (HPLC: 5%, GC: 16–23%). It works well with small sample amounts, as for instance from sediment cores and aerosol collectors, and requires less sample preparation work than the GC method. Moreover, the here presented HPLC method facilitates 13C and 14C analyses on PyC from environmental samples.