Southern blight disease, caused by the fungal pathogen Athelia rolfsii, suppresses plant growth and reduces product yield in Cannabis sativa agriculture. Mechanisms of pathology of this soil‐borne disease remain poorly understood, with disease management strategies reliant upon broad‐spectrum antifungal use. Exposure to chitosan, a natural elicitor, has been proposed as an alternative method to control diverse fungal diseases in an eco‐friendly manner. In this study, C. sativa plants were grown in the Root‐TRAPR system, a transparent hydroponic growth device, where plant roots were primed with .2% colloidal chitosan prior to A. rolfsii inoculation. Both chitosan‐primed and unprimed inoculated plants displayed classical symptoms of wilting and yellowish leaves, indicating successful infection. Non‐primed infected plants showed increased shoot defense responses with doubling of peroxidase and chitinase activities. The levels of growth and defense hormones including auxin, cytokinin, and jasmonic acid were increased 2–5‐fold. In chitosan‐primed infected plants, shoot peroxidase activity and phytohormone levels were decreased 1.5–4‐fold relative to the unprimed infected plants. When compared with shoots, roots were less impacted by A. rolfsii infection, but the pathogen secreted cell wall‐degrading enzymes into the root‐growth solution. Chitosan priming inhibited root growth, with root lengths of chitosan‐primed plants approximately 65% shorter than the control, but activated root defense responses, with root peroxidase activity increased 2.7‐fold along with increased secretion of defense proteins. The results suggest that chitosan could be an alternative platform to manage southern blight disease in C. sativa cultivation; however, further optimization is required to maximize effectiveness of chitosan.