The molecular encapsulation of two purine derivatives, caffeine and acyclovir by hydroxypropyl-β-cyclodextrin (HPBCD) in water solution has been studied at 25 °C by fluorescence spectroscopy. When the inclusion complex is formed, changes in the fluorescence spectra of the drugs enable the calculation of the association constants of the binding process, by using a nonlinear regression analysis of the experimental data at three different λem. The inclusion of the drugs into the CD cavity has been supported by preliminary docking studies. The resulting binding constants have been also discussed in terms of the control release of both purine derivatives, evaluating the HPBCD herein studied as a suitable vector for these drugs.