A picture would be helpful, especially a closeup of where the two stems meet. It sounds like a sucker from the root stock has grown up into what appears like a second tree. The one with white flowers is most likely the rootstock. See where the stems meet and if I'm correct, I'd consider cutting the lower of the two.

It sounds like you have a cherry that has had the "weeping" scion wood grafted on top of a "standard" or regular cherry stem. The regular stem has suckered and the upright branches will bloom with the characteristics of that tree; the weeping scion will bloom with the characteristics of the grafted wood. I would not hesitate to prune ALL of the upright branching off at the branch collars where the stems meet the main trunk, continuously. This will promote the grafted weeping wood. There may have been a bad "take" at the high graft which would make the trunk or "standard" try to sucker, so this may be a regularly repeated process. If you do not do the pruning, the weeping cherry will be overtaken by the type of cherry that the standard wants to be. Hope this makes sense.
hortster

Definitely a bad graft with the standard cherry suckering. This happens to a lot of ornamental fruit trees. You'll have to cut the white flowered trunk off at the collar (just past where it meets the main trunk).

It sounds like both trunks are the same size? That means this problem started as soon as you planted it. A picture would help a lot.

Make a CLEAN cut on an ANGLE just past the branch collar. It is probably too thick to use loppers, so purchase a decent pruning saw (Lowes, HD sell these), and make a starter cut at the bottom of the branch, angling up and in toward the tree, then do the rest of the cut from the top of the branch, angling toward the bottom cut (away from the tree). The cut is on an angle to shed water. You must do a cut on the bottom first so that when you cut from the top it doesn't pull down and rip the bark along the main trunk, which can kill the tree.

Do this now or wait until next year and do it in early spring before the buds break. Do not wait much longer, because right now the cherry will use it's energy to heal the wound, but if you wait until May or later it will have used most of it's energy in flowering and growing new branches and will not heal quickly at all.

The standard cherry will grow about 20 feet high. Depending on the rootstock, it may even bear fruit. Standard cherries are hardy trees, and it will definitely end up killing your weeping graft if you don't get rid of it soon.

As for it looking odd, don't worry, in a few years the weeping tree will grow to the other side with proper pruning. Right now the other tree is preventing it from growing that direction. Once it is gone the other side will start to thrive. The sun exposure alone will help a lot. Don't expect too much this year though, since it will be focusing its energy on healing.

Weeping part will fill in on its own, without pruning. In fact, since cutting back reduces overall volume of growth after pruning it would slow evening out to cut the weeping top back.

Like many other kinds of trees flowering cherry trees do best with as little pruning as possible, except where there is a substantial problem such as a dead or rubbing branches. Whatever serious pruning may appear advantageous while tree is still in training at the grower's nursery, specimens entering the retail phase and being planted by final consumer are usually beyond this phase.

About three years ago I was given a weeping cherry tree and since then it has grown taller than expected with one long branch growing at a 45 degree angle and I was wondering if I cut that off will it kill the tree.

hey preacher

proper pruning will never kill .. and otherwise healthy tree ...

start your own post.. insert a picture.. and we can give you some real guidance ...

the trees ability to encapsulate and heal itself.. is a matter of faith .... dont you think ...

ken