Trypanoplasma borreli is an extracellular parasite that is transmitted by a leech vector and is naturally found in the blood of cyprinid fish. High parasitemia and associated severe anemia together with splenomegaly are typical of infection of common carp, Cyprinus carpio L. Papain-like cysteine proteinases expressed by trypanosome parasites contribute to the pathogenicity of trypanosomes, and are considered an important target for the development of new trypanocidal drugs. T. borreli is a member of the Parabodonida, sharing a common ancestor with the other Kinetoplastida. We demonstrate the presence of a cysteine proteinase expressed by T. borreli. Alignment of the sequence with other kinetoplastid cysteine proteinase sequences supports the phylogenetic hypotheses based on analyses of ribosomal RNA genes. We expressed the T. borreli cysteine proteinase in Escherichia coli, refolded the purified protein into a biologically active proteinase and showed it has cathepsin L-like activity. Addition of the (non)active proteinase to in vitro-derived carp head kidney-derived macrophages did not significantly modulate macrophage activity. Immunization of carp with the recombinant proteinase did induce a very high increase in proteinase-specific antibodies but only slightly lowered parasitemia. Digestion of host hemoglobin and immunoglobulin by the cysteine proteinase likely contribute to the pathogenicity of T. borreli. The possibility that digestion by the cysteine proteinase of host transferrin could contribute to an innate activation profile of macrophages in vivo is discussed. Our findings suggest a conservation of function with respect to cysteine proteinase activity in the Parabodonida in support of the hypotheses on the phylogeny of the Kinetoplastida.