I had to add an additional "End IF" to cover "Else IF" statement the full query be like this :
CREATE PROCEDURE `SP_DeleteFileInfo`(IN pFileID int)
BEGIN
Set @FileRef= null;
select filesinfo.ReferenceID into @FileRef FROM filesinfo where filesinfo.FileID =pFileID;
DELETE From filesinfo WHERE filesinfo.FileID= pFileID;
IF EXISTS(SELECT * from filesrefrences where filesrefrences.ReferenceID= @FileRef and filesrefrences.RefrenceCount>1) then
update filesrefrences
set filesrefrences.RefrenceCount= filesrefrences.RefrenceCount-1
where filesrefrences.ReferenceID= @FileRef;
SELECT @FileRef;
ELSE IF(@FileRef is Not NULL) THEN
DELETE from filesrefrences WHERE filesrefrences.ReferenceID = @FileRef;
SELECT -77;
ELSE
SELECT -99;
end if;
end if;
END;