Abstract Narcolepsy is a sleeping disorder, caused by selective loss of neurons secreting a wake-promoting hormone, hypocretin (HCRT). Increased narcolepsy incidence was noted in China after the peak of 2009 H1N1 pandemic influenza (pH1N1) cases and in Europe after Pandemrix vaccine administration. The causes of HCRT neuron depletion and its relationship with pH1N1 are unknown. As narcolepsy susceptibility is associated with HLA-DQ6 and with a TCR α gene (J24) polymorphism, we hypothesized that abnormally expanded J24+/CD4+ T cells in DQ6+ subjects mediate autoimmunity against HCRT neurons and that molecular mimicry (epitopes in pH1N1 and self-antigens) drives T cell expansion via DQ6 presentation. We reported the in vivo expansion of DQ6/HCRT87–97–reactive J24+/CD4+ clones using a J24 allele and an un-conventional phenotype in patients compared to related clones in DQ6+ controls. Here, DQ6/peptide binding and crystal structure identify an epitope, HA274–287 from pH1N1 hemagglutinin, with homology to HCRT87–97 and another peptide, HCRT1–13. DQ6/HA274–287 tetramers isolated >2000 tetramer+/CD4+ T cells in DQ6+ subjects. Single-cell sequencing of TCRs and 25 phenotypic transcripts identify a DQ6/HA274–287 tetramer+/J24+ clone with the identical TCR clonotype (TCR27) and phenotype as the expanded DQ6/HCRT87–97–reactive J24+ clones previously found in the same patient. Control-derived TCR27+ clones identified by DQ6/HCRT1–13 or DQ6/HCRT25–37 tetramers are unexpanded and lack expression of any of the phenotypic genes. Our findings show that DQ6+ subjects carry J24+/CD4+ cells, both public and cross-reactive (e.g TCR27). TCR27 expansion in patients argues for molecular mimicry as a factor in narcolepsy immunopathogenesis.