This paper presents elemental data of sediment samples and its analysis methodology. The samples were collected from Central Karakoram—an unexplored region in Pakistan. Surface sediment samples (0–10 cm) were collected from 9 different locations along the Hunza River in Central Karakorum at an average altitude of 1,561 m covering almost 100 km length along the river. Samples were analysed by the k 0-insturmental neutron activation analysis and the activation constant method for 34 elements (Al, As, Ba, Ca, Ce, Co, Cr, Cs, Dy, Eu, Fe, Ga, Hf, K, La, Mg, Mn, Na, Nd, Rb, Ru, Sb, Sc, Se, Sm, Sr, Ta, Tb, V, Yb, Zn, Zr, Th and U). The analysis methodology was discussed with important sources of nuclear and fission product interferences. The important components of uncertainties identified were the k 0-factor, Q 0-factor, detector efficiency and counting statistics. The methodology was validated by analyzing the IAEA-S-7 (soil) and IAEA-SL-1 (lake sediment) reference materials. The mass fraction data was explored by principal component analysis. Measured elemental mass fractions were compared with the similar data from other locations of the world. It was shown that anthropogenic activities have little influence on the elemental distribution in the sediment.