Alpha-tocopherol, an essential dietary supplement, synthesized by photosynthetic organisms is the most biologically active antioxidant component of vitamin E in humans. Attempts to improve the yield of alpha-tocopherol using plant cell cultures has gained significance in recent years. Here, we developed a high alpha-tocopherol yielding cell line of Helianthus annuus using a model based metabolic engineering approach. To this end, we adapted an available genome-scale model of Arabidopsis for simulating H. annuus metabolism using constraint-based analysis to identify and rank suitable enzyme targets for overexpression. Of the various model-predicted enzyme targets, majority belonged to the vitamin E pathway and the MEP pathway while the others included reactions from the nucleotide biosynthesis and amino acid metabolism. Experimental validation of the top strategy (overexpression of p-hydroxyphenylpyruvate dioxygenase,) resulted in a high alpha-tocopherol yielding transformed cell line (up to 240 μg g−1), which was ≈10-fold more than in the untransformed cell line. A cell suspension was developed from the selected transformed cell line for in vitro production of alpha-tocopherol, which resulted in a maximum alpha-tocopherol yield of 412.2 μg g−1 and titre of 6.4 mg L−1.We thus demonstrate the utility of model-based metabolic engineering for multi-fold yield enhancement of commercially important plant secondary metabolites. © 2019 Elsevier B.V.