HKDF is used in one of my projects to derive separate keys from a common master key. But profiling has shown it to be the performance bottleneck under certain circumstances. Is there any faster alternative? The only things I get after googling "key derivation function" are HKDF and password stretching algorithms like PBKDF2 or scrypt.
If you are using the full HKDF each time, you could possibly save time by only using the Extract portion once and Expand once per derived key. That could even halve the total time taken, if you had a worst case situation.
Another speedup possibility within HKDF is to use another hash. Either a faster hash or one that matches the required key length better. For example, if you are generating a 256-bit key you would likely not want to use SHA-1 even though it is faster than SHA-256, because you would need two serial iterations.
Depending on the use case, you might also want to look into using KDF1 or KDF2, which are faster hash-based KDFs. They are defined in ISO18033, but KDF1 is also in RFC 3447 (appendix B.2), under the name MGF1.
However, as explained in the HKDF paper (pdf), the Expand scheme could work with any PRF. That means that for best performance you could roll your own version by replacing HMAC with a block cipher that you have in hardware (e.g. AES-NI on some new CPUs), since secure block ciphers are indistinguishable from a PRF up to the birthday bound.