We present a scanning probe microscopy technique for spatially resolving transport in cold atomic gases, in close analogy with scanning gate microscopy in semiconductor physics. The conductance of a quantum point contact connected to two atomic reservoirs is measured in the presence of a tightly focused laser beam acting as a local perturbation that can be precisely positioned in space. By scanning its position and recording the subsequent variations of conductance, we retrieve a high-resolution map of transport through a quantum point contact. We demonstrate a spatial resolution comparable to the extent of the transverse wave function of the atoms inside the channel and a position sensitivity below 10 nm. Our measurements agree well with an analytical model and ab initio numerical simulations, allowing us to identify a regime in transport where tunneling dominates over thermal effects. Our technique opens new perspectives for the high-resolution observation and manipulation of cold atomic gases.