The antileukemic drug asparaginase, a key component in the treatment of acute lymphoblastic leukemia, acts by depleting asparagine from the blood. However, little is known about its pharmacokinetics and mechanisms of therapy resistance are poorly understood. Here, we explored the in vivo biodistribution of radiolabeled asparaginase, using a combination of in vivo imaging and biochemical techniques, and provide evidence for tissue specific clearance mechanisms, which could reduce effectiveness of the drug at these specific sites. In vivo localization of Indium-111-labeled E.coli asparaginase was carried out in C57Bl/6 mice by both microSPECT/CT and by ex vivo biodistribution studies. Mice were treated with liposomal clodronate to investigate the effect of macrophage depletion on tracer localization and drug clearance in vivo. Moreover, macrophage cell line models RAW264.7 and THP-1, as well as cathepsin B deficient mice, were used to identify the cellular and molecular components controlling asparaginase pharmacokinetics. In vivo imaging and biodistribution studies showed a rapid accumulation of asparaginase in macrophage-rich tissues such as liver, spleen and in particular bone marrow. Clodronate-mediated depletion of phagocytic cells markedly prolonged the serum half-life of asparaginase in vivo and decreased drug uptake in target organs. Immunohistochemistry and in vitro binding assays confirmed the involvement of macrophage-like cells in the uptake of asparaginase. We identified the activity of the lysosomal protease cathepsin B in macrophages as a rate-limiting factor in degrading asparaginase both in vitro and in vivo. We show that asparaginase is rapidly cleared from the serum by liver, spleen and bone marrow-resident phagocytic cells. As a consequence of this efficient uptake and protease mediated degradation, particularly bone marrow resident macrophages may provide a protective niche to leukemic cells.