Yes, but it will take a while. I had a wallet with 13,000 keys and it ran for 3 days.
wow, are you sure it take 3 days to import 13,000 keys ?
so i think it's faster using this command
cat privkeyfile | while read privkey; do ./bitcoind importprivkey $privkey mylabel false ; done
it was only take about 4 hours to import 20,000 keys.