Oocytes are dependent on messenger RNA (mRNA) stores that accumulate during their follicular development to support the transcriptionally dormant events of meiosis. However, during maternal ageing, oocytes are known to experience alterations in mRNA abundance: a phenomenon that contributes to reduced developmental potential. Here we have investigated whether small non-protein-coding RNA (sRNA) accumulation is similarly altered in aged mouse oocytes. Further, we assessed whether such changes could potentially influence gene expression in aged oocytes. High throughput sRNA sequencing revealed substantial changes to the profile of the global sRNA population of germinal vesicle (GV) stage oocytes from young (4-6 weeks) and aged mice (14-16 months). Among the changes documented, 160 endogenous small-interfering RNAs (endo-siRNAs) and 10 microRNAs were determined to differentially accumulate within young and aged oocytes. We further demonstrated that these differentially accumulated endo-siRNAs putatively targeted 39 unique mRNAs. More specifically, we discovered that the encoding transcripts of two members of the kinesin protein family, Kifc1 and Kifc5b, were selectively targeted for expression regulation by three endo-siRNAs of elevated abundance in aged GV oocytes. Accordingly, we also revealed a reciprocal decrease in Kifc1 and Kifc5b mRNA expression as well as a reduction of their encoded protein, HSET, in aged GV and metaphase I stage oocytes. The implications of a reduction in functional HSET protein was explored using complementary siRNA-mediated knockdown of Kifc1 and Kifc5b and pharmacological inhibition of HSET from the GV stage, both of which led to increased rates of aneuploidy in otherwise healthy young metaphase II oocytes after in vitro maturation. Taken together, our data raise the possibility that an altered sRNA profile, specifically an altered endo-siRNA profile, could contribute to the age-related decline in oocyte quality.