Nevado del Huila is an active volcano in Colombia having high explosive potential and serious hazard for surrounding population. Here we present the first 3‐D seismic velocity model of the Nevado del Huila Volcanic Complex based on local earthquake tomography. We used 13,790 events with the corresponding 49,412 P wave and 47,972 S wave arrival times recorded by the Volcanological and Seismological Observatory of Popayán (Colombia). The period of observations from 2007 to 2016 covers stages of eruptions (first registered to date) and repose of the volcano. The seismic structure reveals two prominent nearly vertical anomalies with high Vp/Vs ratio that are interpreted as conduits connecting the volcano structures with a deeper seated magma reservoir. The anomaly beneath the southern flank of the volcano is limited by the Calambayú Fault and coincides with the dense seismicity cluster. We interpret this anomaly as the pathway of fluids following the weakened rocks along the fault zone. Another anomaly located beneath the main summit of Nevado del Huila probably represents the magma conduit that fed the previous eruption of this volcano. The seismicity here is not as intensive as that beneath the southern flank, which is possibly caused by higher temperature and ductile properties of rocks in the conduit. At depths from 2 to 4 km below surface, we observe the limit between higher Vp/Vs below and lower Vp/Vs above that possibly represents the level of fluid degassing due to decompression.