We use the Pristine survey CaHK narrow-band photometry, combined with the Sloan Digital Sky Survey (SDSS)ugr photometry, to provide a cleaner sample of blue horizontal branch stars in the Galactic halo out to large distances. We demonstrate a completeness of 91 per cent and a purity of 93 per cent with respect to available spectroscopic classifications. We subsequently use our new clean sample of these standard candles to investigate the substructure in the Galactic halo over the Pristine footprint. Among other features, this allows for a careful tracing of multiple parts of the Sagittarius stream, providing a measurement independent from other tracers used and reaching larger distances. Moreover, we demonstrate with this clean and complete sample that the halo follows a density profile with a negative power-law slope of 3.5-4.0. As the relatively shallow SDSS u band is the limiting factor in this technique, we foresee large potential for combining Pristine survey photometry with the much deeper u-band photometry from the Canada-France-Imaging Survey.