Egg quality is an important aspect in rainbow trout farming. Previous studies have shown that many environmental factors impact egg quality. However, the most obvious effects on egg quality were associated with post-ovulatory ageing of the eggs. The objective of this study was to identify miRNAs that are involved in controlling egg quality using post-ovulatory aged eggs. Egg samples from females on day 1, day 7, and day 14 post-ovulation, which had the embryonic survival rates of 95%, 75% and 35%, respectively, were collected and small RNAs isolated from these samples were subjected to deep sequencing using the Illumina platform. The massive sequencing produced 1,966,612, 3,185,985, and 1,801,518 reads from day 1, day 7, and day 14 eggs, respectively. A total of 755 known miRNAs were identified and an additional 153 novel miRNAs were predicted from this dataset. Based on the normalized sequencing reads, 87 differentially expressed miRNA were identified, with 61 being highly expressed in day 14 eggs, and 26 being highly abundant in day 1 eggs. Real-time PCR analysis of a selected number of miRNAs confirmed 6 miRNAs that were highly expressed in either day 1 or day 14 eggs. Each of these miRNAs were predicted to target 7 to 114 genes that are mostly involved in regulation of E2F1, retinoblastoma hypophosphorylation, cell growth, germinal center reaction and immune response. Further characterizations of these miRNAs and their target genes may provide valuable information on the role of these miRNAs in controlling egg quality in rainbow trout.