Nikon D5500 audio problems?

Total beginner here. I need to be able to make videos with my camera, but I can't figure out the audio. Every time I make a video, the sound ends up sounding muffled. Most of what is heard sounds like a running fan or something and what I'm saying is barely heard in the background.

That's why you should buy a camcorder for video.
If your camera can take an external mike, try that, but you're wasting a superb stills machine on a purpose for which it was never designed.

If your primary task is shooting video, then you bought the wrong product. You need a camcorder with an external mic. Input, not a DSLR.

One of the problems with using DSLRs for video is they pick up internal noises such as the lens focusing motor. Try using an external mic, a field recorder or, best of all, use a camcorder.

If you're serious about getting good audio you'll get an external microphone -- either a wired or wireless that plugs into the jack on your camera, or use a separate sound recorder such as the Zoom H1 or H2 and merge the audio with your video in your editing software.
As other people have mentioned, a DSLR is not the best choice for video. So far you seem to have encountered only one of the several disadvantages.

What you have is an image capturing device. The whole concept of its design was never meant to do video so try not to expect decent audio from it.
- Audio out of TV (headphone jack) into Nikon D3300 audio in for video?
- Best way to sell a slightly almost new DSLR camera? Nikon d5500? 18-55 mm lens?
- Which 2 lenses do i buy with nikon d5500?
- Looking for input on which Nikon camera I should get- D3300, D5300, or D5500?
- Dhould i Buy Nikon D5500 as my first DSLR?