Coached by Des Hasler and captained by Ben Kennedy, competed in the National Rugby League's 2006 Telstra Premiership.
The Sea Eagles finished the regular season 5th (out of 15), reaching the finals where they were knocked out in the second week by the St. George Illawarra Dragons.
In an away final against the Newcastle Knights, the Sea Eagles led at halftime only to see their lead run down in a controversial second half.
Although they did advance a week further, the Sea Eagles' season ended with a 28–0 shutout at the hands of the St. George Illawarra Dragons.
At the 2006 Dally M Awards Manly's Ben Kennedy, who will retire at the end of the season, was named lock and captain of the year.