It doesn't look to happy, does it! Is this Meyer lemon? Repotting is a good idea. Check for roots that are circling in the container and will not be able to spread out in the new pot. You want to prune those back so that they do not continue to circle in the new pot. You don't want to remove a lot of root mass, but circling roots or roots growing into each other will interfere with the uptake of water and nutrients. Citrus is also picky about pH, doing best typically between 6.5 and 6.0, or a bit lower. If your tap water is alkaline, you may want to adjust the pH of any tap water you use to water it, or collect rain water. Potted citrus will also do best in a well draining potting mix with a regular fertilizer routine, using a balanced fertilizer that includes micronutrients which are not supplied long term by potting mixes.

But you asked about pruning. Lemon trees can be trained to a single trunk or they can be allowed to branch out like it is doing, producing several "trunks" rising at an angle. I don't do a lot of pruning generally for potted citrus, but you can train them to that single trunk if you want. I would remove weak or crossing branches, thinking about what you want it to ultimately look like. Don't remove more that a quarter of the canopy. If a branch is getting too long or leggy, head it back by pruning off the tip of the branch, back to a bud that is facing the direction you want a new branch to grow. You can also train a branch to a new orientation. For example, if you want a more upright trunk, you can gently bend the trunk to be more upright and use some strategy or another to loosely secure it in that new orientation.

Let me know if you have further questions, and enjoy your tree!