AbstractSelection and internalization of cargo via clathrin‐mediated endocytosis requires adaptor protein complexes. One complex, AP‐2, acts during cargo selection at the plasma membrane. African trypanosomes lack all components of the AP‐2 complex, except for a recently identified orthologue of the AP‐2‐associated protein kinase 1, AAK1. In characterized eukaryotes, AAK1 phosphorylates the μ2 subunit of the AP‐2 complex to enhance cargo recognition and uptake into clathrin‐coated vesicles. Here, we show that kinetoplastids encode not one, but two AAK1 orthologues: one (AAK1L2) is absent from salivarian trypanosomes, while the other (AAK1L1) lacks important kinase‐specific residues in a range of trypanosomes. These AAK1L1 and AAK1L2 novelties reinforce suggestions of functional divergence in endocytic uptake within salivarian trypanosomes. Despite this, we show that AAK1L1 null mutant Trypanosoma brucei, while viable, display slowed proliferation, morphological abnormalities including swelling of the flagellar pocket, and altered cargo uptake. In summary, our data suggest an unconventional role for a putative pseudokinase during endocytosis and/or vesicular trafficking in T. brucei, independent of AP‐2.