The contract sees Wilkinson playing a sixth season with Sydney FC, and the 36-year-old is hungry for more silverware as he seeks a fourth A-League crown.
The Sky Blues lost this year's A-League grand final to Melbourne City.
"I'm feeling good and I'm extremely pleased to be captaining this fantastic group of players once more," Wilkinson said in a statement.
"With the FFA Cup returning and another AFC Champions League campaign to contend with, plus our challenge for more premiership and championship titles, it's going to be a tough and very exciting season."
The defender has missed only three A-League games in five seasons, two when the coach decided to rest him, and he was the only Sydney FC player to play every second of last season.
Wilkinson has won more premierships (5) than any player in Australian National League history since 1977, and he holds the A-League record for most finals appearances (27) and grand finals (7).
He is one of only five players to make 300 appearances in the A-League, despite having missed three seasons playing in Korea.
Sydney FC coach Steve Corica praised Wilkinson's ability and desire to win, describing him as one of the best players Australia has produced.
"We are very fortunate to have Wilko, and our success in recent times has been in no small part down to him," Corica said.
"He is showing no sign of slowing down, and his performances will be key in leading our club to more success next season and I'm delighted he is returning."