No one, and probably no one will. To be fair Pele claims he scores 1200 goals but he counts the goals he made in unofficial matches and tournaments. He play a lot of games in lesser regional competition, as there was no official Brazilian tournaments until later in his career. He also did many tours around the world with Santos, playing unranked teams. If you just take a look at official games his record might be around 600. The so 1200 goals is an exaggeration, is like start counting the goals you score at training.
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Everybody answers Pele because he's the most well known one. In actuality its another Brazilian called Arthur Friedenreich from the 1920's. He's reported to have scored over 1200 goals in over 1200 games, though the exact number is not known. He was also the first ever black player to play Football.
Check under the Top Scorer topic in the "Related Links" section.
Here is an updated list:
Josef Bican 1468 goals+
Gerd Muller 1461 goals
Artur Friedenreich around 1363 goals
Pele 1284 goals
Franz Binder around 1040 goals.
Only two footballers Pele and Romario have scored 1000 goals, though all of Romarios goals are not counted.