Amorphous silica is an abundant gangue mineral in ore deposits, but its effect on mineral flotation is unknown. In this study, the effect of amorphous silica on pulp rheology and chalcopyrite flotation was investigated. It was found that the presence of amorphous silica increased the pulp viscosity more significantly than quartz especially at a high percentage of solids. This is due to the formation of network structures of amorphous silica particles driven by hydrogen bonds between silanol (Si OH) groups on adjacent silica units. Flotation tests were conducted using mixtures of chalcopyrite, quartz and amorphous silica. The copper recovery was not affected when the percentage of amorphous silica was less than 30 vol%. However, it started to decrease significantly after the percentage of amorphous silica was further increased, which was caused by the significantly increased pulp viscosity. Although a low percentage of amorphous silica had little influence on copper recovery, it caused a significant increase in mass recovery, leading to the decreased copper grade. This was found to be due to the increased entrainment of gangue minerals resulting from the low particle density of amorphous silica and the network structures formed by amorphous silica particles.