In medical research, continuous markers are widely employed in diagnostic tests to distinguish diseased and non-diseased subjects. The accuracy of such diagnostic tests is commonly assessed using the receiver operating characteristic (ROC) curve. To summarize an ROC curve and determine its optimal cut-point, the Youden index is popularly used. In literature, estimation of the Youden index has been widely studied via various statistical modeling strategies on the conditional density. This paper proposes a new model-free estimation method, which directly estimates the covariate-adjusted cut-point without estimating the conditional density. Consequently, covariate-adjusted Youden index can be estimated based on the estimated cutpoint. The proposed method formulates the estimation problem in a large margin classification framework, which allows flexible modeling of the covariate-adjusted Youden index through kernel machines. The advantage of the proposed method is demonstrated in a variety of simulated experiments as well as a real application to Pima Indians diabetes study.