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We sequenced and analyzed the complete mitochondrial genome of <i>Lentipes ikeae</i> and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of <i>L. ikeae</i> was determined using the Illumina HiSeq X Ten sequencing platform, and the gene structural characteristics and base composition were analyzed. Based on the mitochondrial genome sequences of 28 Sicydiinae species published in GenBank and mitochondrial protein-coding genes (PCGs), <i>Acanthogobius flavimanus</i> (Gobionellinae) was selected as an outgroup to construct phylogenetic trees of Sicydiinae using the maximum likelihood and Bayesian inference methods. The mitochondrial genome of <i>L. ikeae</i> (GenBank number: OP764680) has a total length of 16,498 bp and encodes 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop (control) region. Gene rearrangement is not observed. The mitochondrial genome of <i>L. ikeae</i> exhibits an AT preference, with AT skew > 0 and GC skew < 0 across the entire genome. The phylogenetic relationships of Sicydiinae based on 13 mitochondrial PCG sequences are <i>Sicydium</i> + (<i>Stiphodon</i> + (<i>Sicyopus</i> + <i>Lentipes</i>)) + <i>Sicyopterus</i>, indicating that <i>Sicydium</i>, <i>Sicyopterus</i>, <i>Lentipes</i>, and <i>Stiphodon</i> are all monophyletic groups.