Fibroblast activation protein (FAP) is an important target for the integrated diagnosis and treatment of tumors. However, FAP-targeted small molecule-based radiopharmaceuticals often face challenges such as low tumor uptake and short tumor retention, which hinder their biomedical and clinical applications. In this study, two radiolabeled FAP-targeted nanoprobes based on melanin nanoparticles (MNPs) were designed and developed in order to evaluate their potential for FAP-targeted theranostics. The excellent metal ion complexing property of melanin allowed 89Zr to be efficiently labeled on the MNP platform. After PEGylated MNPs were modified with small molecules FAPI-04 and GPFAPI-04 and radiolabeled with 89Zr to obtain [89Zr]Zr-F-MNPs and [89Zr]Zr-GPF-MNPs, these two nanoprobes achieved active targeting through FAPI ligands. The radiochemical purity of 89Zr-labeled nanoprobes remained above 90% in fetal bovine serum (FBS) solution in 72 h. In vitro experiments showed that both [89Zr]Zr-F-MNPs and [89Zr]Zr-GPF-MNPs were taken up by FAP high-expressing U87MG cells (2.58 ± 0.07% vs 3.00 ± 0.10% for 2 h; 2.93 ± 0.08% vs 3.62 ± 0.04% for 4 h). For the in vivo study, at 48 h postinjection (p.i.) of the nanoprobe, the U87MG tumor uptake of [89Zr]Zr-F-MNPs and [89Zr]Zr-GPF-MNPs reached 4.83 ± 0.50% ID/g and 5.13 ± 0.38% ID/g, respectively. Blocking experiments further confirmed the FAP-dependent targeting ability. Neither of the two nanoprobes elicited observable adverse effects in vivo. In conclusion, the FAPI-MNPs-based nanoprobe platform, which integrates active targeting and passive accumulation, improves tumor uptake and retention time of FAP-targeted radioligands with excellent biosafety. This study offers a new strategy and platform for the development of FAP-targeted diagnostic and therapeutic probes with promising clinical translation potential.