I'll second PiedmontGirl, they can get the fold-up stroller from you at the end of the jetway, just before you walk on the aircraft. That said, I've also seen some airlines that will let you fold it up and take it onboard for storage in an overhead bin. If it's a full flight, expect the former, versus the latter.
Two other factors to consider...
1/ Ask the agents if you can pre-board. Nearly every airline allows families traveling with small children to go down the jetway in advance of the overall passenger group, and you'll be much less stressed getting her out of the stroller, seated, and your stuff stowed if you're not looking up and seeing all those folks behind you. (They'll still be up in the gate area).
2/ Consider a seat towards the front of the aircraft. When it comes to aircraft with wing-mounted engines (737, Airbus), any seat -aft- of the wing is going to have more ambient noise than one forward of the wing, and that noise sometimes startles or scares small kids, especially on landing when reverse thrust is used. Aircraft with tail-mounted engines (DC-9, MD
-80, regional jets) are not much of a problem in this regard, unless you're in the very last row or two of the aircraft.
One of the other things I found helpful with my kids at that age was to be ready to point out stuff out the window. If they started looking fretful and appeared to be about to "lose it", I'd immediately point to the window and get them to notice another airplane, a funny-looking cloud, or -anything- to divert their attention, since fear often self-induced.
ALL views, opinions expressed are mine ONLY and are NOT representative of those shared by Southwest Airlines Co.