If you are talking about web access - yes, JIRA can be configured to run over SSL - see here. Cloud JIRA runs over SSL only.
Thank you so much.
I mean also in comunication between Application Server and database ?
That doesn't matter - the database is only accessible internally.
For on-premise you should design your internal landscape in such a way that the database server is never accessible from the outside. In this case you should not need SSL, but just in case you are freaked out about internal leakage of information or you need to adhere to some IT standard that requires SSL, you should be able to enable SSL in the JIRA configuration. If this is possible at all and how to do it really depends on the type of database you are using and the JDBC driver JIRA is using.
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