Long non‐coding RNAs (lncRNAs) generally display tissue‐specific distributions, and testis‐specific lncRNAs form the highest proportion of lncRNAs in many species. Here, we presented a detailed analysis of testis‐specific lncRNAs in the melon fly, Zeugodacus cucurbitae, a highly destructive insect pest of cucurbitaceous and other related crops. Most testis‐specific lncRNAs were found to be long intergenic non‐coding RNAs (lincRNA). The size distribution of these lncRNAs ranged between 600 and 1000 nucleotides. Testis‐specific lncRNAs that harboured one isoform number and two exons were the most abundant. Compared to other male tissues, the testis had more highly expressed lncRNAs. The quantitative real‐time polymerase chain reaction results of 10 randomly selected testis‐specific lncRNAs showed expression patterns consistent with RNA‐seq data. Further analysis of the most highly expressed testis‐specific lncRNA, lnc94638, was undertaken. Fluorescent in situ hybridization assays localized lnc94638 to the apical region of the testis that contains mature spermatozoa. RNA interference‐mediated knockdown of lnc94638 expression reduced spermatozoa numbers and impaired the fertility of Z. cucurbitae male. This study provides a catalogue of testis‐specific lncRNAs, shows that the testis‐specific lnc94638 is involved in spermatogenesis and has the potential to be used for treating male sterility.