Peptide amphiphiles (PAs) previously designed in our laboratory are known to self-assemble into nanofibers that exhibit bioactivity both in vitro and in vivo. Self-assembly can be triggered by charge neutralization or salt-mediated screening of charged residues in their peptide sequences, and the resulting nanofibers can form macroscopic gels at concentrations as low as 0.5% by weight. Controlling the kinetics of gelation while retaining the bioactivity of nanofibers could be critical in tailoring these materials for specific clinical applications. We report here on a series of PAs with different rates of gelation resulting from changes in their peptide sequence without changing the bioactive segment. The pre-existence of hydrogen-bonded aggregates in the solution state of more hydrophobic PAs appears to accelerate gelation kinetics. Mutation of the peptide sequence to include more hydrophilic and bulky amino acids suppresses formation of these nuclei and effectively slows down gelation through self-assembly of the nanofiber network. The ability to modify gelation kinetics in self-assembling systems without disrupting bioactivity could be important for injectable therapies in regenerative medicine.