The conserved phosphoinositide-dependent protein kinase PDK1 regulates cell growth and stress signaling in eukaryotes. In the fission yeast Schizosaccharomyces pombe, Pdk1 has been linked to cytokinesis, which could point to new functions for this kinase family. Here, we discovered that Pdk1 localizes to eisosomes, which create invaginations in the plasma membrane, in addition to the spindle pole body. Pdk1 promotes phosphorylation of the core eisosome protein Pil1 and regulates eisosome length. Dysregulated eisosomes are not responsible for cytokinesis defects previously observed in pdk1∆ cells. Instead, we found that Pdk1 regulates the localization of the anillin-like protein Mid1 and the protein kinase Sid2, which promotes cytokinesis as part of the septation initiation network. Our combined results provide insights into the role of Pdk1 in eisosomes and cytokinesis, which extend the functions of this conserved protein kinase family beyond canonical growth control pathways.