Campylobacter jejuni (C. jejuni) is one of the main causes of human campylobacteriosis worldwide. Chicken is the main reservoir of C. jejuni. The cecum is the primary site of C. jejuni colonization. Our previous study has shown that the CLOCK gene is important to regulate the response to C. jejuni inoculation and has a cross-talking with immune-related genes. Correlation networks between the CLOCK gene and microRNAs (miRNAs) play vital roles in colorectal tumorigenesis. MiRNAs play crucial roles in bacterial invasion through regulating multiple target genes. To study the regulatory correlation between miRNAs and target genes, 5 miRNAs that regulate the expression of the CLOCK gene (CLOCK-interacted miRNAs) and 5 immune-related target genes predicted through Targetscan and miRDB were selected to analyze the expression pattern in chicken ceca at 4, 8, 12, 16, 20, and 24 h post C. jejuni inoculation using quantitative PCR. The results showed that the expression of gga-miR-148a, gga-miR-1416-5p, gga-miR-30b, and gga-miR-30c were significantly up-regulated at 8 hpi, and gga-miR-30a-5p, gga-miR-30b, and gga-miR-30c were significantly down-regulated at 24 hpi, and gga-miR-1416-5p was significantly down-regulated at 20 hpi (P < 0.05). The expression levels of BCL9 (B-cell CLL/lymphoma 9), STX16 (syntaxin16), IL4R (interleukin 4 receptor), and IRF4 (interferon regulatory factor 4) genes were significantly up-regulated at 8 hpi, while SOCS3 (suppressor of cytokine signaling 3) was significantly down-regulated. Furthermore, the expression pattern of gga-miR-30b was consistent with gga-miR-30c. Both miRNAs and mRNAs showed an oscillation expression pattern in both inoculated and non-inoculated groups. The regulatory direction of SOCS3 was contrary to those of gga-miR-148a, gga-miR-1416-5p, gga-miR-30b, and gga-miR-30c at 8 hpi. In summary, MiR-30 and the miR-148/miR-152 family time-dependently regulate the response to C. jejuni inoculation in chicken ceca. BCL9, STX16, IRF4, and IL4R play important roles in the response to C. jejuni inoculation. The CLOCK gene-interacted miRNA and immune-related target genes had a correlative response to C. jejuni inoculation. The SOCS3 gene interacts with gga-miR-30b, gga-miR-30c, gga-miR-148a, and gga-miR-1416-5p in response to C. jejuni inoculation at 8 hpi. The correlations between CLOCK-interacted miRNA and immune-related target genes play vital roles in the response to C. jejuni inoculation. The results herein will lay the foundation for further study of a regulatory mechanism of chicken miRNAs and their target genes in response to C. jejuni inoculation.