We propose fast tuning of a Fano resonance (FR) in a three dimensional metamaterial (MM). The MM consists of an elliptical nanohole array (ENA) embedded through a metal/ phase-change material (PCM)/metal multilayer. The results show that the interference between the electric and magnetic resonances can be significantly enhanced when the elliptical nanoholes occupy the sites of a rectangular lattice, thus providing a FR with a higher value quality factor (Q) compared to the ENA with a square lattice. By switching the PCM (Ge2Sb2Te5) between its amorphous and crystalline states, the FR peak can be red-shifted by up to 42%. The FR can be tuned with a ultra low energy mid-infrared laser pulse of 0.38 ns duration and an intensity of 3.2μW/μm2.