MicroRNAs (miRNAs) are small non-coding RNAs involved in gene regulation and are potential biomarkers for several diseases, including canine enteropathies. While metabolite profiling and microbiome in canine enteropathies have been previously explored, data on miRNA expression remain limited. This study aimed to profile miRNA expression in Yorkshire Terrier canine enteropathy using Illumina sequencing and quantitative PCR (qPCR) to compare miRNA levels between sick and healthy dogs from fecal samples. Despite the hypothesis that disease-related alterations in miRNA levels would differentiate sick dogs from controls, no significant differences were observed between the groups in either sequencing or qPCR analyses. These findings suggest that miRNA profiles may not vary significantly in the context of Yorkshire Terrier enteropathy and indicate that other molecular or metabolomic markers may be more indicative of disease state. This study also indicates that fecal samples may not be an ideal sample type for miRNA profiling. This study contributes to the understanding of molecular signatures in canine enteropathies and provides a basis for further research into alternative biomarkers for diagnosis and monitoring.