Hi robaugh27, sorry to hear about this problem.

Is the unwanted pinned site a search engine shortcut, the type that puts something like @amazon in the address bar?

If so, there is a separate option for removing those:

(1) In a new tab, type or paste about:config in the address bar and press Enter/Return. Click the button accepting the risk.

(2) In the search box in the page, type or paste improve and pause while the list is filtered

(3) Double-click the browser.newtabpage.activity-stream.improvesearch.topSiteSearchShortcuts preference to switch the value from true to false

(4) If Firefox doesn't blank it out, double-click the browser.newtabpage.activity-stream.improvesearch.topSiteSearchShortcuts.havePinned preference to display an editing field, delete its contents, then press Enter or click the blue check mark button to save the change.

If not, you could clear all the pinned sites as follows:

(1) In a new tab, type or paste about:config in the address bar and press Enter/Return. Click the button accepting the risk.

(2) In the search box in the page, type or paste browser.newtabpage.pinned and pause while the list is filtered

(3) To clear the list, either:

(i) Find the trash can at the right end of the row and click it; or

(ii) Double-click the preference to display an editing field, delete its contents, then press Enter or click the blue check mark button to save the change.

More info on about:config: Configuration Editor for Firefox.

Thank you. The first part of your solution worked and not only did it clear the duplicate item, "Amazon", it was then replaced by a missing pinned item, "youtube". Perfect!