Pedrazzini's departure follows that of Domenico Scala, who was also on the compensation sub-committee and who quit as head of audit and compliance last month.
The sub-committee sets compensation rules and compensation for FIFA's president, Gianni Infantino, the members of its supervisory Council and FIFA's secretary general, according to FIFA statutes agreed in April.
It is made up of the chairpersons of the finance and the audit and compliance committees plus a third member jointly appointed by the two chairpersons.
FIFA did not give a reason for Pedrazzini's departure. Asked for comment, Pedrazzini confirmed his resignation from the sub-committee but declined to comment on the reason.
His departure had been reported earlier by Swiss newspaper Handelszeitung.
Infantino's proposed pay has made headlines, with the Frankfurter Allgemeine Zeitung reporting leaked details of FIFA Council meetings that it said showed he had been angered by an offer of 2 million Swiss francs ($2.09 million) a year.
The FIFA president has said his salary has not been decided and would be less than 2 million.
Infantino replaced Sepp Blatter this year, with FIFA battling to haul itself out of the worst graft scandal in its history.
The Swiss-based body has been embroiled in crisis since last year with 42 people, including former FIFA executive committee members, and entities indicted in the United States.
($1 = 0.9581 Swiss francs)
(Reporting by Joshua Franklin and Brian Homewood; editing by Andrew Roche)
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