Can you at least run away?
If not this sounds like a real bummer.

What the weird mage that herds cats said.

PC or console?

If PC then go here http://elderscrolls.wikia.com/wiki/Console_Commands_(Skyrim) hit CTRL + F and type in bounty, use the command to clear it.

Make sure to be in a different hold when you do it.

Like some other people already said...If you had the option to tell them that you're the thane(not jarl) of Whiterun, you should be able to serve your sentence in the jail or pay your bounty.

One time a dragon attacked solitiude and I must have hit one of the guards by accident because as soon as it died they all atacked me (infront of castle dour) and none of them would let up and it had been a while since my last save. Long story short I killed all the guards that were attacking me when it became clear that they sheathing my weapon was going to do nothing. And then I walked up to a guard in another part of the city who actually talked and let me pay my (now huge) fine. Hope that helps cant hurt to try since if it doesnt work you can reload and your back in the same situation again anyway. Other thing is maybe running out of the city until you can fast travel and coming back much later to see if anything changed.

If all else fails i would DEFINATELY use console commands and "fix" the situation before i gave up on a high level character.

why not run? or let them arrest you?

Well after taking a break cause it was pissing me off, I went back after 72 hrs, and they still tried to arrest me. I said I was the Jarl, and they backed off, then when I got into the city, they did it AGAIN, I said ok I will pay the fine..... it was 0, f*cking 0!!!!!!!!!
I clicked to pay it, it wouldn't accept it, and I had to run. Tried it again, no deal. And this is on a 360, so consul commands don't work.

Yea just kill them all and leave no witnesses

Man u trolling hard, U obviously can't be the Jarl of Whiterun...

just kill them and forget about it. God, theres like how many other towns? How difficult would it really be to just forget about it and then make a run for your items in your house whenever you need them. If your lv 49 I am pretty sure you have done anything whiterun has to offer anyway.

Check your active effects. You probably became a vampire without noticing.

mostly THIS

You probably have a bounty in some other hold its a known bug that means guards from different holds will attack you. The only way around it I know of is to pay all your bounty's also a bug sometimes kicks in that means even if you have no witnesses the next guards you see will attack you anyway.

i remember first time playing FNV when i was on 1 life and a glowing one about to hit me i accidenlty hit save instead of load i had to completely restart

lol [censored] THIS