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Abstract We analyse the single top production in association with the Higgs at the Large Hadron Collider (LHC) using Standard Model (SM) effective operators upto dimension six. We show that the presence of effective operators can significantly alter the existing bound on the top-Higgs Yukawa coupling. We analyse events at the LHC with 35.9 and 137(140) fb −1 integrated luminosities using both cut-based and machine learning techniques to probe new physics (NP) scale and operator coefficients addressing relevant SM background reduction. The four fermi effective operator(s) that contribute to the signal, turn out to be crucial and a limit on the top-Higgs Yukawa interaction in presence of them is obtained from the present data and for future sensitivities.