Small non-coding RNAs (sncRNAs) present in the conditioned medium (CM) of bovine preimplantation embryos are potential noninvasive biomarkers for assessing embryo quality. Accurate quantification of sncRNA levels in the spent CM is of utmost importance in this regard. RT-qPCR is considered as the gold standard for quantifying RNA. In order to standardize RT-qPCR data in the sample type under investigation, the use of suitable stable sncRNAs is essential. Here, we selected 10 sncRNAs from small RNA sequencing of CM samples derived from both bovine blastocysts and degenerate embryos, and evaluated their expression stability together with that of cel-miR-39 as a spike and the often-used U6 small nuclear RNA at different embryo developmental stages. In CM of 2-cell embryos, rsRNA-1044 showed the most stable expression, while tDR-1:32-Gly–CCC–1 was the most stable expressed sncRNA in CM of the stages beyond the 2-cell stage. Next, tDR-1:32-Gly–CCC–1 was used for normalizing the RT-qPCR data from the CM of blastocysts and degenerate embryos. Bta-miR-155 and tDR-39:75-Arg-CCG-2 were found to be significantly up-regulated in the CM of blastocysts compared to that of the degenerated embryos (P = 0.028 and P = 0.017, respectively), suggesting their expression levels are related to embryo development stage. In conclusion, tDR-1:32-Gly–CCC–1 can serve as a suitable reference sncRNA for normalization of RT-qPCR data of the CM from bovine blastocysts. •tsRNAs but not microRNAs are abundant in bovine preimplantation embryo conditioned medium (CM).•rsRNA-1044 is the most stable small non-coding RNA in the CM of the 2-cell embryo.•tDR-1:32-Gly–CCC–1 exhibited the best expression stability in the stages beyond the 2-cell stage.•bta-miR-155 and tDR-39:75-Arg-CCG-2 are significantly up-regulated in the CM of blastocysts compared to degenerates.