Henderson is trying to obtain LPGA Tour status for 2016, and will instead opt to compete in qualifying for the LPGA's Marathon Classic in Ohio.
The tournament in Ohio is held on July 16-19, the same week as the Pan Am Games golf competition at Angus Glen Golf Club in Markham, Ont.
"Since turning professional in December, my goal has been to play in as many LPGA Tour and Symetra Tour events as possible to earn LPGA status and avoid the Q-School process," the Smith Falls Ont., said in a statement. "
"After winning the Four Winds Invitational last week, LPGA Commissioner Whan graciously granted me membership on the Symetra Tour which allows me the opportunity to earn my way onto the LPGA. I am now guaranteed a spot in a professional tournament the week of July 13. Based on my goals for the year, this is an opportunity I cannot pass up."
"As an ambassador for golf in Canada, I am disappointed to miss the Pan Am Games. I am so appreciative for the support I receive every week from Golf Canada and fans across the country. I wish the competitors all the best and look forward to cheering them on."
Henderson, 17, won the Four Winds Invitational last week, becoming the third-youngest winner in Symetra Tour history.
Working to replace Henderson
In a statement, Golf Canada said it will work with the Canadian Olympic Committee to determine who will replace Henderson and join Lorie Kane of Charlottetown.
Henderson has competed in seven LPGA events as a non-member, posting two top-10 finishes and five top-25 results. She recently finished in a tie for fifth at the KPMG Women's PGA Championship and was tied for 10th at last year's U.S. Women's Open.
"We are disappointed to lose Brooke Henderson from the Pan Am golf team but we respect the rationale that went into this very difficult decision," said Golf Canada chief sport officer Jeff Thompson. "Brooke is committed to her goal of reaching the LPGA Tour and her recent play, including her victory on the Symetra Tour last weekend, has provided a unique opportunity that will help her achieve that goal.
"We will continue to be a strong supporter in her career."
The Canadian men's Pan Am golf team will be comprised of Austin Connelly, a dual citizen who lives in Irving, Texas, and Garrett Rank of Elmira, Ont. Golf will make its Pan Am debut at the Angus Glen Golf Club in Markham, Ont., ahead of the sport's return to the Olympic program next year in Rio.
"As an ambassador for golf in Canada, I am disappointed to miss the Pan Am Games," Henderson said. "I am so appreciative for the support I receive every week from Golf Canada and fans across the country. I wish the competitors all the best and look forward to cheering them on."
The Pan Am field will include 32 women and 32 men. There will be women's individual, men's individual and mixed team events.
With files from The Canadian Press