Background <p>Magnetic Resonance Enterography (MRE) has emerged as a tool in diagnosing and monitoring Crohn’s disease. Despite its importance, no comprehensive bibliometric analysis has focused on MRE’s impact in this field. This study addresses this gap by analyzing the 100 most-cited articles related to MRE in Crohn’s disease, revealing key trends and influential research in the field.</p> Methods <p>Two independent researchers utilized Scopus to identify relevant articles using predefined keywords. The articles were ranked by citation count, and detailed bibliographic data was collected. Advanced statistical analyses were conducted to identify research trends and evaluate article influence using citation metrics.</p> Results <p>Our study analyzed trends from 1990 to 2024, revealing a peak in research activity between 2008 and 2018, with the most articles (<i>n</i> = 52) published in 5 years from 2010 to 2014. Citation activity mirrored the trends with 100 most cited articles between 2008 and 2016, peaking in 2011 at nearly 7000 citations with a sharp decline after 2016. No significant correlation (<i>p</i> = 0.40) was identified between citation count and journal impact factor. Our study identified the shift in past research trends from fluoroscopy to MRE and the saturation in research on MRE in recent years.</p> Conclusion <p>Our study highlights a shift from fluoroscopy toward advanced MR techniques for managing Crohn’s disease.</p> Advances in knowledge <p>Our study highlights a shift from fluoroscopy to MRE research in recent years. However, the plateau in MRE research underscores the need for innovative investigative approaches and novel research directions.</p> Graphical abstract <p></p>