Since you haven't had any answer for almost a week, I thought I might give it a shot. This method works for creating a Trash folder; it might work for Junk as well.

See https://support.mozilla.org/en-US/kb/profiles-tb#w_how-to-find-your-profile to locate your profile.

Using your File Explorer, go to your profile and the look at the level below that for Mail or ImapMail (depends on whether you use POP or IMAP). Then in whichever folder, find your INBOX. In the same folder, if you have a Junk.msf file, delete it (or rename it Junk.bak). Delete the Junk folder in Trash.

Check your Account Settings -> Junk Settings to specify where junk messages are to go.

Restart TB and see if that fixes it: mark something as Junk and see where it goes.

Since you give no hint of what you tried, have you tried dragging it back in place and dropping it there?

Airmail said

Since you give no hint of what you tried, have you tried dragging it back in place and dropping it there?

Yes I tried drag and dropping the folder with no success. Even after it was moved, Edit>Undo didn't work.

duggabe said

Since you haven't had any answer for almost a week, I thought I might give it a shot. This method works for creating a Trash folder; it might work for Junk as well. See https://support.mozilla.org/en-US/kb/profiles-tb#w_how-to-find-your-profile to locate your profile. Using your File Explorer, go to your profile and the look at the level below that for Mail or ImapMail (depends on whether you use POP or IMAP). Then in whichever folder, find your INBOX. In the same folder, if you have a Junk.msf file, delete it (or rename it Junk.bak). Delete the Junk folder in Trash. Check your Account Settings -> Junk Settings to specify where junk messages are to go. Restart TB and see if that fixes it: mark something as Junk and see where it goes.

I think this fixed it.

The See https://support.mozilla.org/en-US/kb/profiles-tb#w_how-to-find-your-profile to locate your profile. kept bringing me to the wrong folder.

Thank you guys for the help;

Looking on your picture I wonder if its not an IMAP account? If so just subscribe to the junkmail. Did you moved your profile directory ? Curious how come its not in %appdata%\roaming\thunderbird\profiles\??????.default\