Apparatus and methods are provided for flaring a stent deployed within a branch vessel including an ostium communicating with a main vessel, a first end of the stent extending at least partially from the branch. A catheter is provided that includes a first balloon carried on its distal end, and a second balloon that includes a distal section overlying at least a portion of the first balloon and a proximal section. The catheter distal end is introduced into the main vessel and positioned through the ostium and stent into the branch until the first balloon is disposed within the stent. The first balloon is expanded to anchor the stent, and the second balloon is expanded to flare the first end of the stent. Optionally, the first balloon is expanded further, e.g., to expand the stent within the branch body lumen and/or dilate the lesion.