I haven't tried but found something in my documentation.
(1). External break point in R3 before calling RFC
(2). Login into APO system and external break point in RFC.
(3). Activate remote debugging via transaction code SRDEBUG
Refer note 1766428 to have better Idea (which mentions transaction SRDEBUG is obsolete)
Hope it helps.
Message was edited by: Sravan Guduru