Introduction Artificial intelligence (AI) chatbots, including ChatGPT and DeepSeek, are becoming popular tools for generating patient education materials for chronic diseases. AI chatbots are useful as supplements to traditional counseling but lack the empathy and intuition of healthcare professionals, making them most effective when used alongside human therapists. The objective of the study is to compare ChatGPT-4o and DeepSeek V3-generated patient educational guides for epilepsy, heart failure, chronic obstructive pulmonary disease (COPD), and chronic kidney disease (CKD). Methodology In this cross-sectional study, the standardized prompts for each disease were entered into ChatGPT and DeepSeek. The resultant texts were evaluated for readability, originality, quality, and suitability. Unpaired t-tests were performed to analyze statistical differences between tools. Results Both AI tools created patient education materials that had similar word and sentence counts, readability scores, reliability, and suitability in all areas, except for the similarity percentage, which was much higher in ChatGPT outputs (p=0.049). The readability scores indicated that both tools produced content that was above the recommended level for patient materials. Both tools resulted in high similarity indices that exceeded accepted academic thresholds. Reliability scores were moderate, and while understandability was high, actionability scores were suboptimal for both models. Conclusion The patient education materials provided by ChatGPT and DeepSeek are similar in nature, but neither satisfies recommended standards for readability, originality, or actionability. Both still need additional fine-tuning and human oversight to enhance accessibility, reliability, and practical utility in clinical settings.