My B string doesn't sound right?

So I just got my guitar from my uncle and tuned it up. It's correctly tuned, I checked everywhere. However, when I press the string on the 3rd fret and strum, the sound comes out all wrong. I'm trying to learn Good Riddance by Green Day, and it involves plucking that string, but when I compare the two notes, they sound nothing alike. What seems to be the problem?