They are having a promotion on a site (not Disney) where you get your ticket upgraded to a 5 day park hopper with the purchase of a 3 day. We need 6 day tickets so my question is, can we upgrade this ticket to a six day once in the parks or can you only do that if you purchase the tickets through Disney? The answer is probably obvious but just making sure!

Yes... you can upgrade your ticket. See guest services before you first use it to do the upgrade
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My MIL did this recently with tickets purchased from Undercover Tourist.

But would you have to pay for the 3 to 6 upgrade, or just the 5 to 6? I know sometimes at DL you only get credit for what you actually paid.

But would you have to pay for the 3 to 6 upgrade, or just the 5 to 6? I know sometimes at DL you only get credit for what you actually paid.

Good question! Anyone? :)

Im not sure but, I would be prepared to pay anything above and beyond what you actually paid for the ticket, regardless of days. Take your receipt with you just to make sure you at least get that amount credited.

Granted, I would think that you should only have to pay for the extra day, plus tax, but I am not 100% sure.

When you first use a MYW ticket in any turnstile it will immediately lock the value of the ticket at the Current Gate Price (CGP), no matter what you paid for it. If you do an upgrade once the ticket is partially used Disney will absorb the difference between what the ticket was originally sold for and the CGP. All you will have to pay is the difference between the CGP of the ticket(s) you are trading in and the CGP of the new ticket(s), plus tax.

If you have not used the ticket, when you go for an upgrade you will have to pay the difference between what Disney originally sold the ticket for and the CGP of the upgraded ticket you are purchasing.

It is always better to use the ticket first. Note that you have a 14 day window to do any upgrades once a ticket had been used, even if the No Expire option has been purchased.

Also, anything that needs to be done with tickets may be performed at any park (including water parks and TTC) ticket booth or any Guest Relations Office (including DTD). You can also do most ticket transactions at the Lobby Concierge of the Disney resorts, but cannot do anything there related to any sort of Annual Pass.

And to answer the OP's question briefly, if you use the ticket prior to upgrade you will only pay the difference between the CGP of a 5-day and of a 6-day ticket (which is $2.13 including tax).