Before Pythia - sexual reproduction
After Pythia - looms
After "Lungbarrow" - sexual reproduction
Other timelines/continuitites - sexual reproduction.
The Pythia are not mentioned in the TV show. So far as the show is concerned, Time Lords seem to have reproduced in much the same way we do, although the subject has never been dealt with in detail. The Pythia, looms, etc. Are in some novels but not in others -- and the novels are not required to be consistent with each other. This makes it impossible to give a single coherent answer to the question.