It doesn’t seem to exist a ready-made solution for exporting Endnote Bibliography to JabRef, and since many are wondering how to transfer their bibliography, this blog article provides a solution.
First, go to http://www.zotero.org/ and download Zotero standalone or Zotero plugin for Firefox.
To export your Endnote bibliography in RIS format: In the menu Edit > Output Styles > Open Style Manager… select export to RefMan (RIS) Export (the Bibtex Export does not seem to work fine in my system but you can give it a try just save the file as Bibtex <library.bib> and try to open it from JabRef). The export this from the File > Export Menu (make the appropriate selections in the dialog).
You may also follow the instructions found here, to import a bibliography into Zotero from Endnote.
Then Export this to Refer/Bibix and store it to your bibliographies folder and open this by using JabRef and save your bibliography from JabRef.