Additional and complementary mineral exploration boreholes are often designed to obtain valuable information about mineralized intervals with the least cost. In this research, a new multi-criteria approach is proposed to design the optimum additional directional boreholes in a 3D environment in the second stage of drilling. The proposed algorithm consists of six steps. In the first step, based on the ore deposit type, exploration stage and available exploration data, the main criteria for the selection of the complementary boreholes are identified. In the second step, 3D geological models associated with the identified criteria are prepared. In the third step, a set of 3D candidate complementary boreholes is designed. In the fourth step, scores along the candidate borehole, relevant to various criteria, are estimated. In the fifth step, the candidate boreholes are ranked using a multi-criteria decision-making algorithm and an optimum borehole is selected for further drilling. Finally, information of new borehole is added to the earlier available data and the above steps are repeated to select additional borehole until a stopping condition for drilling is fulfilled. The proposed algorithm is applied at the Dalli Cu–Au porphyry deposit to design optimum boreholes for further drilling. The considered criteria for designing the additional boreholes are based on magnetic susceptibility, logged hydrothermal alteration, mineralized intervals, length of barren rocks, depth of mineralized intervals, Cu and Au grades along the earlier boreholes and trenches, kriging variance and drilling cost. By using the proposed method, four additional boreholes are designed. These boreholes are located in zones of highest uncertainties and highest grades. By drilling these four boreholes, the accuracy of the grade model is improved by 15%. The proposed approach employs all earlier exploration data to improve designing new boreholes in various deposit types and different stages of drilling.