He was selected as the top player in a vote of the membership over Brad Bryant, R.W. Eaks, Loren Roberts and Denis Watson.
Denis Watson, who won twice, including the Senior PGA Championship, earned Champions Tour Rookie of the Year honors. Watson finished third on the money list with 12 top-10 finishes and collected his award over fellow nominees Fred Funk, Scott Hoch, Mark OMeara and Nick Price.
Eaks was named the Champions Tour Comeback Player of the Year after winning the first two titles of his career. The 55-year old Eaks finished sixth on the money list with a career high $1,534,098. He topped Hoch and Denis Watson for the award.
The Champions Tour Byron Nelson Award for low scoring average went to Roberts for the second consecutive season. On his way to winning the Charles Schwab Cup, Roberts posted a scoring average of 69.31.
Flanagan, a native of Australia, became the first international player in the 18-year history of the Nationwide Tour to earn top honors. He won three times in only 17 starts to earn an automatic promotion to the PGA TOUR. Despite playing the last several months of the season on the PGA TOUR, Flanagan still finished third on the Nationwide Tour money list with $369,951.
He was selected over a field that included Richard Johnson and Roland Thatcher, both two-time winners in 2007.