Usually it involves a conflict where your logical mind tells you not to do something, but you are drawn by something else to do the opposite. Against my better judgement I got back together with my ex. (I know she's bad for me, but I just can't resist her.)

Use the phrase when you do something that you believe you shouldn't do, because you do not think it is sensible or wise. For example, eating an entire package of junk food in one sitting: "Against my better judgement, I ate the whole bag of chips." or "I ate all the cookies, against my better judgement." Or staying up late when you have an early appointment the next day: "Against my better judgement, I was up until 1AM playing video games."

Against my better judgement = despite thinking it was a bad idea. Structures: Against my better judgement, I did X. I did X, against my better judgement. E.g.: Against my better judgement, I let him go to the concert. I opened the door to the stranger, against my better judgement.

It’s usually used after you’ve already done something that you regret. You knew it was a bad idea but for whatever reason you did it anyway, and now you are saying that you should have followed your gut instinct and not done it.