Aging-related erectile dysfunction (A-ED) is a neurovascular and refractory disorder with complicated pathophysiological mechanisms and a high prevalence. MicroRNAs (miRNAs), which modulate a variety of cell functions, may be involved in the pathophysiological processes of this disorder. To investigate the miRNA profile in the corpus cavernosum (CC) of aging rats with ED, and to analyze the target genes and signaling pathways regulated by the dysregulated miRNAs. According to the apomorphine test, the experimental animals were divided into three groups: aging rats with ED (group AE), aging rats with normal erectile function (group AN), and young rats as normal controls (group YN). After the erectile functional test, CCs from each group were then collected for histological and molecular measurements. Intracavernous pressure response to electric stimulation of the cavernous nerve was used to evaluate erectile function. Histological changes within CC were evaluated using immunofluorescent staining. GeneChip array was used to analyze the miRNA expression profiling. The miRNA profilings were further validated by real-time polymerase chain reaction. The TargetScan or DAIAN web platform and DAVID were used for bioinformatic analysis. Accompanied with significantly decreased erectile function, the content of smooth muscle and endothelium within the CC of rats with A-ED was significantly decreased compared with both AN group and YN group. miR-1, miR-200a, miR-203, and miR-206 were found and validated up-regulating with above twofold change in AE group. According to the bioinformatics analysis, the four up-expressing miRNAs could regulate eNOS/NO/PKG and PGE1/PKA pathways through regulating 13 target genes. Four miRNAs were found up-regulated significantly in the CC of rats with A-ED. The four miRNAs might play important roles in the development of A-ED by regulating the eNOS/NO/PKG and PGE1/PKA pathways despite lots of experiments still need to be validated.