Satoru Fujii started one game for the San Angelo Colts of the independent Central League in 2003. Despite not giving up a single hit, he lasted only one inning after walking six batters, throwing a wild pitch and allowing three runs - two of which were earned - to score. He took the loss in the game, which would prove to be the only one of his minor league career.
He also played in the Hoofdklasse in the Netherlands. In 2005, he was 8-7 with a 2.02 ERA for Sparta/Feyenoord with a .203 opponent average and 112 K in 124 2/3 innings, though he walked 64. He finished 10th in ERA (between Roger Kops and Nick Stuifbergen), 5th in opponent average, third in wins (behind Rob Cordemans and Richard Orman), led in innings, led in complete games (8 in 16 starts), led in whiffs (14 more than runner-up Patrick Beljaards), led in walks (10 more than runner-up Diegomar Markwell), tied for the most quality starts (14, even with Cordemans and Orman) and tied for the most shutouts (3, even with Orman, Cordemans and David Bergman).
Returning in 2006, Fujii was 8-7 with a 3.12 ERA for Sparta/Feyenoord, walking 71 in 129 2/3 innings. He was 8th in opponent average (.233), tied Gregory Gustina for fifth in victories, was second in innings (trailing Cordemans barely), tied for first in starts (18, with Cordemans), led in complete games (8), was second with 105 strikeouts (22 behind Cordemans), led in walks (22 more than anyone else) and led with four shutouts (double countrymate Akira Okamoto).