A rational drug design approach led to the synthesis of three pairs of enantiomers derived from the peroxisome proliferator-activated receptor (PPAR) pan agonist AL29-26, identifying (S)-2 as a potent and selective PPARα partial agonist. Molecular docking and molecular dynamics simulations elucidated the binding modes of (S)-2 within the ligand-binding domains of PPARα and PPARγ. In vitro, (S)-2 demonstrated significant anti-steatotic effects, upregulating key PPARα target genes involved in lipid metabolism. In vivo, (S)-2 exhibited hypolipidemic and antihyperglycemic activity in a diabetic mouse model, outperforming fenofibrate in lowering blood glucose and lipid levels, while showing no toxicity in major organs (artery, kidney, liver, pancreas). The therapeutic effects of ((S)-2 were attributed to its PPARα selectivity, reduced activation of PPARγ, and mild protein tyrosine phosphatase 1B (PTP1B) inhibition. These findings highlight (S)-2 as a promising lead compound for the development of safer and more effective treatments for dyslipidemic type 2 diabetes.