The feeding of Hessian fly can manipulate wheat plant physiology differentially between compatible and incompatible reactions. In the current study, we infested a wheat genotype ‘Molly’ with a virulent Hessian fly biotype vH13 and an avirulent biotype GP separately to study the differential expression of wheat genes in glycolysis and its related metabolic pathways through Northern analysis. We also quantified the content of major substrates and metabolites that are associated with glycolysis. Our study indicated that glycolysis pathway was induced during the compatible reaction but slightly suppressed during the incompatible reaction. The induction of glycolysis during the compatible interaction may be an important step for Hessian fly to manipulate wheat physiology in a way that favors its development, while the suppression of glycolylsis during the incompatible reaction could be associated with the resistance mechanism in wheat plants to Hessian fly infestation.