Henderson, from Smiths Falls, Ont., opened her second round with a 3-under 32 and followed it with back-nine birdies on the par-5 13th and par-4 17th holes to grab the outright lead at 5-under 137. The 16-year-old has played near flawless golf since opening the tournament with an over-par front-nine on Tuesday.
"It was a tough start yesterday being 3-over through eight holes but then I went 4-under the rest of the way which was really huge," said Henderson, the event's defending champion. "I had a couple of moments yesterday that really saved my round and I think that really saved my tournament. Going into today I knew I had momentum and I just wanted to keep that going."
Henderson is one-stroke clear of Augusta James of Bath, Ont., and American Liz Breen, who share second place at 4-under 138 at the conclusion of Wednesday's windy second round.
"It was much tougher today, we were here bright and early and it was quite a bit colder from past days so the ball wasn't quite flying as far," Henderson continued. "The wind also really picked up especially in the middle of my round, I was hitting four clubs more than what I normally do."
James battled back during her closing nine, carding birdies on her final two holes to finish with an even-par 71. Breed held the outright lead for a short time on the back-nine before bogeying two of her last six holes to finish tied with James.
Australia's Su-Hyun Oh posted a 2-over 73 to finish in solo fourth at 2-under 140, while Megan Osland of Kelowna, B.C., and Betty Chen of the United States share fifth place at 1-under par.
In the inter-provincial team competition, Ontario's Henderson, James and Brittany Marchand of Orangeville, soared away from the field to capture the team title. The squad fired a 5-under 137 to finish 15 strokes ahead of Alberta in the 36-hole competition at 10-under par.
In the mid-amateur division (25+), Christina Proteau of Port Alberni, B.C., posted a 6-over 77 to card a two-round total of 153. Proteau currently sits three strokes ahead of Helene Chartrand of Pincourt, Que. In the mid-master division, Chartrand, the defending champion, fired a second round 1-under 70 and currently sits one-stroke ahead of Toronto's Marion Reid at 11-over 153.
The champion of the 101st Canadian Women's Amateur Championship receives an exemption into the 2014 Canadian Pacific Women's Open and also the 2014 U.S. Women's Amateur.