Hyperlipidemia, commonly referred to as a high cholesterol condition, is a significant risk factor for cardiovascular diseases (CVDs), obesity, and metabolic syndrome. This condition involves elevated blood levels of lipids, which can be due to genetic or acquired causes. Researchers are increasingly turning to alternative medicine to tackle this disease. The prime objective of this study was to bring forth an innovative food product with significant anti-hyperlipidaemic potential. Many natural foods contain certain medicinal properties which may exert hypolipidaemic potential when taken on a daily basis. Watermelon (Citrullus lanatus) seeds (WMS) are rich in nutrients and nutraceuticals that may have potent effects against this disease. This research was designed to explore the hypolipidaemic impact of WMS in the form of fortified crackers (WMS-C) given to hyperlipidemic rats. A 21-day therapeutic trial was conducted on 12 male Wister rats divided into three groups: G1: negative control normal rats, G2: positive control high-fat diet fed hyperlipidemic rats, G3: 15% WMS-C fed group with hyperlipidaemic rats. The results demonstrated that incorporating WMS-C into the diet of hyperlipidaemic rats of G3 brought significant improvements in almost all biomarkers when compared to the results of G2. These significantly lowered body weight gain, total cholesterol, triglycerides, and LDL cholesterol in WMS-C group has strengthened its nutraceutical significance against hyperlipidemia and associated metabolic diseases. Therefore, the regular dietary intake of WMS could lower the negative health outcomes of CVDs and its associated health issues.