Fangraphs uses Fielding Independent Pitching (3 true outcomes of strikeouts, walks, and home runs)
Baseball Reference uses ERA I believe.
The difference between the two numbers can be significant, take Greinke and Kershaw.
Fangraphs - Kershaw - 6.6 Greinke - 5.3
Baseball Reference - Greinke - 8.1 Kershaw 5.9