L-type amino acid transporter 1 (LAT1) is selectively expressed in the blood-brain barrier (BBB) and brain parenchyma. This transporter can facilitate brain delivery of neuroprotective agents and additionally give opportunity to minimize systemic exposure. Here, we investigated structure-pharmacokinetics relationship of five newly synthesized LAT1-utilizing prodrugs of the cyclooxygenase inhibitor, ketoprofen, in order to identify beneficial structural features of prodrugs to achieve both targeted brain delivery and low peripheral distribution of the parent drug. Besides, we studied whether pharmacokinetics and bioconversion of LAT1-utilizing prodrugs in vivo can be predicted in early stage experiments. To achieve these goals, we compared the in vitro brain uptake mechanism of prodrugs, rate of BBB permeation of compounds using in situ perfusion technique, their systemic pharmacokinetics and release of parent drug in brain, plasma and liver of mice. The results revealed that both excellent LAT1-binding ability and transporter utilization in vitro can be achieved by conjugating the parent drug to aromatic amino acids such as phenylalanine in comparison to prodrugs with an aliphatic promoiety. The presence of an aromatic promoiety directly conjugated in meta- or para-position to ketoprofen led to LAT1-utilizing prodrugs capable of delivering the parent drug into the brain with higher unbound brain to plasma ratio and reduced liver exposure than with ketoprofen itself. In contrast, the prodrugs with aliphatic promoieties and with an additional carbon attached between the parent drug and phenylalanine aromatic ring did not enhance brain delivery of ketoprofen. Furthermore, we have devised a screening strategy to pinpoint successful candidates at an early stage of development of LAT1-utilizing prodrugs. The screening approach demonstrated that early stage experiments could not replace pharmacokinetic studies in vivo due to the lack of prediction of the intra-brain/systemic distribution of the prodrugs as well as the release of the parent drug. Overall, this study provides essential knowledge required for improvement of targeted brain delivery and reduction of systemic exposure of drugs via the LAT1-mediated prodrug approach.