When you delete an organization, all repositories, forks of private repositories, wikis, issues, pull requests, and Project or Organization Pages are deleted as well.
1. Back up your organization content
Once you delete an organization, GitHub cannot restore your content. Therefore, before you delete your organization, make sure you have a copy of all private repositories, wikis, and issues from the account.
2. Delete the organization
In the top right corner of GitHub Enterprise, click your profile photo, then click Your profile.
On the left side of your profile page, under "Organizations", click the icon for your organization.
Under your organization name, click Settings.
Near the bottom of the organization's settings page, click Delete this Organization.