Yes, you can focus a single photon to a small region. It is done all the time in photonic quantum information experiments. For example, to perform quantum state tomography on the spatial degrees of freedom of a single photon state, it is modulated by a spatial light modulator after which it is focussed onto the end of a single mode optical fibre (core radius of a few micron) which guides it to a detector. Of course you need to prepare the same single photon state over and over again the get all the information you need for the tomography.
The issues with the uncertainty relation is dictated by the Fourier relationship between the spatial mode and its angular spectrum. In that sense, it behaves in exactly the same way that you will get with a classic optical beam. The only reason why the issue is more prominent in quantum experiments is because you can only make one measurement for each single photon.