A few slightly different methods:

perl -0i -wpe's/^/new line\n/' file
perl -0i -wpe'substr $_,0,0,"new line\n"' file
perl -i -wlpe'print "new line" if 1..1' file
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All of the above assume (much like some of the ideas suggested by other people here) that the file already has some content; they will not work if it's completely empty.