Many clinical trials compare one specific treatment to a control or standard treatment. In HIV therapeutics, such fixed-regimen designs may be problematic as individualized treatment regimens are standard practice. Designing and implementing a trial that allows individualized treatment options poses particular challenges. In this example of a clinical trial in NeuroAIDS, it is hypothesized that some antiretroviral drugs [i.e., those that penetrate the blood-brain barrier sufficiently to inhibit HIV in the central nervous system (CNS)] will improve HIV neurocognitive impairment, whereas non-penetrating antiretrovirals will not be as effective in improving neurocognitive function. To test this hypothesis, a uniquely designed strategy trial was developed that consists of three essential components: (1) a scoring system that ranks regimens for CNS penetration based on semiquantitative criteria, (2) committee-established individualized regimen options that allow randomization to opposite ends of the CNS penetration spectrum, and (3) timely implementation across multiple centers via web-based resources. For the proposed trial, the three components are combined with an adaptive randomization scheme to minimize potential confounding by several important factors. A small pilot study demonstrated the feasibility and acceptability to providers. In conclusion, an innovative design can provide solutions to challenging practical issues in trials with multiple treatment options.