Small non-coding RNAs are involved in many important physiological functions in pathogenic microorganisms. Previous studies have identified the presence of non-coding RNAs in the major zoonotic pathogen Campylobacter jejuni, however, few have been functionally characterized to date. CjNC110 is a conserved ncRNA in C. jejuni, located downstream of the luxS gene which is responsible for the production of the quorum-sensing molecule autoinducer-2 (AI-2). In this study, we utilized strand specific high-throughput RNAseq to identify potential targets or interactive partners of CjNC110 in a sheep abortion clone of C. jejuni. This data was utilized to focus further phenotypic evaluation of the role of CjNC110 in growth, motility, autoagglutination, quorum sensing, and chicken colonization in C. jejuni. Inactivation of the CjNC110 ncRNA led to a statistically significant decrease in autoagglutination ability as well as increased motility when compared to wild-type. Extracellular AI-2 detection was decreased in ΔCjNC110, however, intracellular AI-2 accumulation was significantly increased with a concurrent increase in LuxS expression, suggesting a key role of CjNC110 in modulating the transport of AI-2. Notably, ΔCjNC110 also showed a significant defect in the ability to colonize chickens. Complementation of CjNC110 restored all phenotypic changes back to wild-type levels. The collective results of the phenotypic and transcriptomic changes observed in our data provide valuable insights into the pathobiology of C. jejuni sheep abortion clone and strongly suggest that CjNC110 plays an important role in regulation of energy taxis, flagellar glycosylation, cellular communication via quorum sensing, and chicken colonization in this important zoonotic pathogen.