The Shulhan Aruch (O.H. 291:2) rules that the time for Seuda Shelishit begins when the time for Minha starts, which is half an hour after midday. Furthermore, if one had Seuda Shelishit before this time, one’s obligation would not be fulfilled.
It would seem based on the wording of the Shulhan Aruch that as long as it is a valid time for Minha one could have this meal, even if one did not yet pray the actual prayer of Minha. However, the Kaf HaHaim (ibid:15), based on the Zohar and the Arizal, writes that the proper order is to first pray Minha and then have Seuda Shelishit. On a Kabbalistic level, says the Zohar, there is a special light which emanates when one prays Minha and only then is one ready to eat Seuda Shelishit. The Ben Ish Hai (Shana Bet, Haye Sarah, § 14) even says that if one ate Seuda Shelishit before praying Minha, one would not have fulfilled one’s obligation.
On the other hand, Rabbi Ben Zion Abba Shaul (Or LeZion, vol. II, ch. 21, § 7) writes that if one knows that the congregation normally prays Minha right before sunset such that Seuda Shelishit will take place after sunset, it is preferable to eat Seuda Shelishit before Minha. Thus, even though Kabbalah gives preference to eating Seuda Shelishit after Minha, it was his opinion that there are instances when this is not practical. Furthermore, Rabbi Baruch Toledano, who very often quotes the Kaf HaHaim, does not mention his aforementioned opinion, implying that he did not rule that Seuda Shelishit must come after Minha.
Summary: The time for Seuda Shelishit is as of a half hour after midday on Shabbat. The common custom is to have Seuda Shelishit after praying Minha, although strictly speaking, it may be eaten before.