Lentil is an alternative gluten-free source with high protein content. In our study, lentil seeds were germinated to enhance the functional and antioxidant properties of lentil. The raw and germinated lentil flour was obtained from lentil seed and used in cookie production. The germination affected the physicochemical, functional, chemical and morphological properties, and pasting behavior of lentil flour. The results indicated that germination caused positive effects on ash and protein content, total phenolic content (TPC), antioxidant properties, oil absorption capacity, and water solubility index. However, germination caused a decrease in the total dietary fiber and starch content due to the activation of the enzymes during germination. SEM images of the germinated lentil flour proved the degradation of starch. Lentil (raw and germinated) flour cookies and wheat flour cookies (Control) were evaluated in terms of physicochemical, TPC, antioxidant properties, textural properties, and in-vitro glycemic index (eGI) value. Germinated lentil flour cookie exhibited the lowest hardness, lightness, yellowness values, the highest TPC and antioxidant activity, and it had the same effect on eGI with control cookie. Overall results indicated that germination can be used as a natural, sustainable, and cost-effective way to improve the functional, and antioxidant properties of lentil. Germinated lentil flour cookie may be considered as a functional food due to high protein content and antioxidant properties.