I was recently having trouble telling Jira to connect to a named SQL Server instance. Using Jira’s configuration manager, I should be able to use the SERVERNAME\INSTANCENAME syntax like every other modern application. Well, not with Jira. I found the solution and here ya go:
In the database field in the configuration manager, which you can launch from bin\config.bat in the Atlassian Jira Program Files folder, type
Oh, did Atlassian forget to tell you to install Java Runtime Edition on your server? Of course they did… Go ahead and install it if you haven’t, but make sure you pay very close attention and don’t click I Agree to install Yahoo and junkware on your machine. Because, well, Oracle.
This information was lovingly sourced from the comments on: https://confluence.atlassian.com/jira/connecting-to-named-instances-in-sql-server-173435.html