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Sexual growth dimorphism is a common phenomenon in teleost fish. However, the mechanism of this complex phenomenon remains unclear. The fine-patterned puffer (<i>Takifugu poecilonotus</i>; Temminck and Schlegel, 1850) exhibits female-biased sexual size dimorphism similar to other pufferfish. In this study, the transcriptomes of female and male <i>T.</i><i>poecilonotus</i> were sequenced, 285.95 million raw read pairs were generated from sequence libraries. After identification and assembly, a total of 149,814 nonredundant unigenes were obtained with an N50 length of 3538 bp. Of these candidates, 122,719 unigenes (81.91% of the total) were successfully annotated with multiple public databases. The comparison analysis revealed 10,385 unigenes (2034 in females and 8351 in males) were differentially expressed between different sexes of <i>T.</i><i>poecilonotus</i>. Then, we identified many candidate growth- and sex-related genes, including <i>Dmrt1</i>, <i>Sox3</i>, <i>Spatas</i>, <i>Prl</i>/<i>Prlr</i>, <i>fabps</i>, Ghr, and <i>Igf1r</i>. In addition to these well-known genes, <i>Fabp</i>4 was identified for the first time in fish. Furthermore, 68,281 simple sequence repeats (SSRs) loci were screened and identified in the transcriptome sequence of <i>T.</i><i>poecilonotus</i>. The results of our study could provide valuable information on growth- and sex-associated genes and facilitate further exploration of the molecular mechanism of sexual growth dimorphism.