Hi Upendar,
welcome to the Atlassian Community!
There is "no out of the box" available to my knowledge but with some scripting you should get what you want.
The article ("Find the last login date for a user in Jira server") is possible a good starting point. Using those database queries you can show the last login timestamps:
https://confluence.atlassian.com/jirakb/find-the-last-login-date-for-a-user-in-jira-server-363364638.html
After that a script you would have you write and adapt to you own needs can check if the dates are within the past 90 days-timerange. A notification could be done in the same script - or you outsource it to a second script.
In case you want to disable users after 90 days not logged in please consider that this might or might not be possible right away - in case of external user management (Active Directory / LDAP / ...) it will not be possible to deactivate them locally.
Cheers,
Daniel
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