Gluten‐free cookie (GFC) made from rice flour is considered a healthy food for people suffering from celiac disease. This study was aimed at developing GFCs supplemented with highly enzyme‐resistant mung bean starch (HERS) and evaluating their physical properties, in vitro and in vivo digestibility, and organoleptic profiles. The HERS was used to substitute for rice flour at levels of 15%, 20%, 25%, 30%, 35%, 40%, and 45% in cookie making using stevia as a sugar substitute. The shape and surface of GFCs were identical to those of wheat‐based ones, but their color intensity gradually darkened with increasing amounts of HERS. The diameter of rice‐based cookies consistently decreased with a higher concentration of HERS added to the dough, whereas their thickness and volume initially increased but then decreased when the concentration of HERS exceeded 30%. However, their spread ratios exhibited an opposite trend to their thickness. Additionally, the hardness of GFCs increased with higher levels of HERS. These results revealed that rice‐based cookies substituted with 30% HERS exhibited the most appropriate color, appearance, spread ratio, and hardness among other cookies tested. This particular cookie was selected for further evaluation of digestibility and organoleptic profiles. The cookie contained a high amount of resistant starch (28.6%), a moderate concentration of slowly digestible starch (21.1%), and a low level of rapidly digestible starch (50.3%), resulting in a low glycemic index (51.7%). Furthermore, this product was highly rated, with an average score of 7 on a 9‐point scale for all sensory attributes. The rice‐based cookies substituted by 30% HERS were recognized as a gluten‐free and low‐GI product with excellent sensory attributes and health benefits.