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Coronavirus disease 2019 (COVID-19), a global pandemic, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2 and transmembrane serine protease 2 (TMPRSS2) facilitates ACE2-mediated virus entry. Moreover, the expression of <i>ACE2</i> in the testes of infertile men is higher than normal, which indicates that infertile men may be susceptible to be infected and SARS-CoV-2 may cause reproductive disorder through the pathway induced by <i>ACE2</i> and <i>TMPRSS2</i>. Little is known about the pathway regulation of <i>ACE2</i> and <i>TMPRSS2</i> expression in male reproductive disorder. Since the regulation of gene expression is mediated by microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) at the post-transcriptional level, the aim of this study was to analyze the dysregulated miRNA–lncRNA interactions of <i>ACE2</i> and <i>TMPRSS2</i> in male reproductive disorder. Using bioinformatics analysis, we speculate that the predicted miRNAs including <i>miR-125a-5p</i>, <i>miR-125b-5p</i>, <i>miR-574-5p</i>, and <i>miR-936</i> as regulators of <i>ACE2</i> and <i>miR-204-5p</i> as a modulator of <i>TMPRSS2</i> are associated with male infertility. The lncRNAs with a tissue-specific expression for testis including GRM7-AS3, ARHGAP26-AS1, BSN-AS1, KRBOX1-AS1, CACNA1C-IT3, AC012361.1, FGF14-IT1, AC012494.1, and GS1-24F4.2 were predicted. The identified miRNAs and lncRNAs are proposed as potential biomarkers to study the possible association between COVID-19 and male infertility. This study encourages further studies of miRNA–lncRNA interactions to explain the molecular mechanisms of male infertility in COVID-19 patients.