Mycophenolate mofetil (MMF), an ester prodrug of mycophenolic acid (MPA), is widely used as a maintenance immunosuppressive regimen in solid organ transplant patients. It is increasingly used for the prophylaxis and treatment of graft-versus-host disease (GVHD) in hematopoietic stem cell transplantation (HSCT) patients. MPA displays extensive binding to serum albumin and glucuronidation to the inactive MPA-7-O-glucuronide (MPAG). Here, we review and discuss the pertinent information regarding the clinical pharmacokinetics of MPA in HSCT patients. The pharmacokinetics of MPA are altered in HSCT patients with lower oral bioavailability, shorter half-life and higher clearance than those in healthy volunteers and renal transplant recipients. Moreover, clearance may be increased in young pediatric patients. The optimal MMF dosing and preferred targets are still under investigation in HSCT patients due to the substantial intra- and inter-individual pharmacokinetic variability of MPA and broad range of transplants (malignant vs. nonmalignant, related vs. unrelated donor, and human leukocyte antigen mismatch). The complex pharmacokinetics of MPA have partly hampered the efficient use of MMF, and pharmacokinetic studies in HSCT patients have been limited in size and mostly inconclusive. Future research should be multi-institutional and focus on developing clinical decisions with adequate statistical power to improve clinical care of HSCT recipients.