Boron (B) is an essential nutrient required for plant growth and physiological processes. Long-distance B transport is facilitated by the formation of B–polyol complexes. We investigated B uptake and distribution in response to differing levels of exogenous nitrogen supply in the hemiparasitic association between Rhinanthus minor and Hordeum vulgare (barley) and in unparasitised barley and single Rhinanthus plants. In this system, the polyol mannitol is the major assimilate in Rhinanthus, whereas polyols are not detectable in barley. Furthermore, previous studies have shown that the accumulation of polyols within Rhinanthus is negatively affected by the application of exogenous nitrogen. Within the association, the strongest accumulation of B was detected in lateral buds and inflorescences of Rhinanthus, consistent with the greatest B demand in strong sink organs supplied through the phloem that contain high concentrations of mannitol. In the host, the strongest B accumulation was found in xylem-supported leaf lamellae. Roots and sheaths did not accumulate substantial amounts of B, while re-circulation of B through the phloem vessels accounted for only 10% (unparasitised) and 8% (parasitised) of the xylem sap-imported B in the mannitol-free barley hosts. In contrast, 53% (attached) and 39% (in the absence of a host) of the xylem sap-imported B was re-circulated in the phloem in the mannitol-rich Rhinanthus. We therefore present the first quantitative uptake and flow models of long-distance B transport in polyol-rich and polyol-free plants. Our findings are consistent with a close relationship between B re-translocation and mannitol concentrations in phloem vessels.