Understanding the intricate molecular interplay between Brassica hosts and the pathogen Plasmodiophora brassicae, causative agent of clubroot disease, is pivotal for devising effective resistance to this disease in Brassica crops. While existing transcriptomic studies have elucidated the host responses to pathogen infection, a comprehensive analysis employing near-isogenic lines (NILs) remains imperative for better understanding of the resistance mechanisms. In this study, we conducted a comparative transcriptome profiling utilizing clubroot-susceptible (CS-NILs) and clubroot-resistant (CR-NILs) near-isogenic Brassica napus lines, carrying the clubroot resistance of turnip (B. rapa var. rapifera), at 7 and 14 days after inoculation. We observed the upregulation of the genes governing phytohormone signaling, receptor kinases, transcription factors, calcium fluxes, and glucosinolate metabolism in the CR-NILs. In addition, the novel differentially expressed genes (DEGs) pertaining to jasmonic acid, calcium signaling, receptor kinases, and glucosinolate biosynthesis were also observed to be differentially expressed. Based on our results, we propose a comprehensive model delineating the molecular events potentially contributing to clubroot resistance in B. napus CR-NILs. Our findings have contributed to an enhanced understanding of the potential mechanisms involved in clubroot resistance which may have utility in targeted breeding initiatives to mitigate the threat of clubroot disease in Brassica crops including canola.