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Shoulder pain with overhead lifting is a common issue that needs to be dealt with well to avoid long term aggravation. There are a few things going on with shoulder pain overhead: there can be too much volume too soon, poor rotator cuff control, poor lifting mechanics, not enough variance in training, etc.
The thing about the shoulder is that even with good form in overhead lifting, there can still be too much volume (which is why variance in training and periodization is important).
The Common Shoulder to Overhead Lift
The default shoulder to overhead lift is a press, push press, or push jerk with a barbell. There is nothing wrong with this, but if there is shoulder pain using a barbell doing these lifts, we should find a modification that allows for pain free training.
The things we can consider are the apparatus, the degree of shoulder abduction, and the angle of shoulder flexion.
Easy Modifications / Changes
One of the first things to try would be going from a barbell (where the shoulders are abducted and externally rotated in the front rack position) to dumbbells and adducting (bringing your elbows closer) the shoulders. This will change the way the shoulder is stressed and is a great modification.
I actually hate to call this a modification. It is really just another training option. We get so stuck on 'oh this is just a crutch exercise until I can get back to the barbell', but that is faulty thinking. Dumbbell overhead press with a more neutral shoulder position is not a regression of 'worse' or 'easier' exercise. It is just a different way to train pressing that stresses the shoulder differently and that is not a bad thing. That is a good thing. You should be trying to tweak lifts constantly to avoid always applying the same training stimulus (that is where the term 'overuse injury' comes from).
The second thing to try if you can't find a pain free overhead press with any apparatus is doing a kneeling or split stance landmine press. This puts the shoulder in a similar position as the dumbbell press, but the angle at which you are pressing overhead is less (the variable being tweaked). This allows for a similar training stimulus but without the need to get as high overhead. There is nothing wrong with this by the way. You can train your shoulders in beneficial ways without pressing just straight forward (bench press) or straight upward (military press).
We have this 'all or none' mentality where if it isn't one of those two lifts, it isn't good. But it is good. Training the different angles provides a different stimulus that is healthy for us over time.
Learn more about how to modify workouts and exercises safely here.