I'm afraid that I have to disagree with Mikkel and Anna. 'I did not use to know this fact' is the negative form of 'I used to know this fact'. Although 'did not use to' is probably less common than 'did not used to' these days, it's obviously more correct grammatically. The 'used to' form is generally used to refer to habits and states in the past , so it's little odd to use it to talk about knowledge of a fact. So the second sentence is unusual, but it's not wrong. And to answer your question, Ali - there is no difference in meaning.

Hi Ali, I did not know this fact - You would say this if somebody told you something you didn't know before. 'I did not use to know this fact' is not grammatically correct. You could say: 'I never knew that ..... until recently.'

UPDATE: I have changed the original text of my answer. The first sentence is correct. The second sentence is also grammatically correct, but I personally find it odd and I wouldn’t recommend that you consider using it until you have a thorough understanding of English. Then you can decide yourself if it’s odd or not.