Harpers Ferry in the fall has great foliage, Been there many many times. I think the walk through the town and up the hills to the church and cemetary will make you weary. I would do a park a day. Wasn't much to see in Antietam except a field and a bridge but that was yrs ago things may have changed.
Mark K makes a point, but I want to bring it more to your attention. Harpers Ferry can be a lot of walking. There is very limited parking, so you may end up down the road at the National Park lots where is is about a half-mile back to town. They do offer buses if you don't want to do the walk. When in town, the streets are steep. VERY steep, so walking up and down will take more effort than a typical stroll around an old town. If you are fit, it shouldn't be an issue. If you have mobility issues, a bum knee, a few extra pounds, etc., it can be more of a challenge.
One of my favorite vacations was Harper's Ferry, it was the first vacation that I took with my now, husband. This a beautiful time of year to go. To answer your question, yes, you can do both Harper's Ferry and Antietam in a day. The downtown historical part of Harper's Ferry isn't that big, but there's a park also. The great thing is that it's all run by the National Park Service, so all the historical stuff is free! ( unlike Gettysburg... ) And food and everything is reasonably priced, the most expensive part of your trip will be your hotel, which can get pricey depending on what time of year. And there isn't much to Antietam. I would start early and plan on a full day to get both in, but it can be done. Not nearly as much walking as Gettysburg and I'm in WV, so that steep hill that's in Harper's Ferry is nothing! One more thing, we ended up parking at the train station that's in Harper's Ferry, wasn't too bad of a walk.
You can do both in a day assuming you are not an avid Civil War fan.
It's unlikely you will find parking in Harper's Ferry proper. Take the bus shuttle from the National Park's parking area. The town is small, maybe city three blocks. It's a step back in time. Check the National Park Service web site to check their schedule
Charles Town is next to Harper's Ferry, minutes away. It has more hotels because of the casino at the race track. Even if you don't gamble it's interesting to visit the casino (and free to get in). If the horses are running it's something to see. Not a lot of people attend just for the races so you can get 20 feet away from the track and feel the thunder of their feet. It's exciting even if you don't have money on them.You don't have to spend all evening there. And again, no charge.(Check their web site to make sure there are no special shows/promotions when you are there. The place will be packed)
If I could make a suggestion, Shepherdstown, WV is a great place to stay within an easy drive of Antietam Battlefield, Harpers Ferry and Charles Town. It is historic in its own right, has a few lodging choices, many more dining options than any of the other towns, and you are right in between Antietam and Harpers Ferry.
Frederick MD is a convenient option for HF/Antietam; lovely downtown area with many dining and shopping options. I agree with an earlier poster who recommended Shepardstown, WV as it is a lovely little town.
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