Background: Three-dimensional (3D) cell models may bridge the gap between two-dimensional (2D) cell cultures and animal models. Technical advances have led to the development of 3D-bioprinted cell models, characterized by greater reproducibility and the ability to mimic in vivo conditions. Glioblastoma multiforme (GBM) is a highly aggressive brain tumor with poor clinical outcomes due to its heterogeneity, angiogenic activity, and invasiveness. Src family kinases (SFKs) play a crucial role in GBM progression, making them attractive targets for drug development. Here, we show results about the pharmacological profile of a new prodrug synthesized from a Src inhibitor, SI306. Methods: Three-dimensional-bioprinted GBM cell models were used in predicting the antitumor activity of the prodrug SI306-PD2 with respect to its precursor, SI306. Results: Since the prodrug releases the active inhibitor through the cleavage by specific enzymes, SI306-PD2 was analyzed for stability and release kinetics in various media, including fetal bovine serum (FBS), which is normally used in cell culture. In comparison to SI306, SI306-PD2 demonstrated higher solubility in water, higher permeability across gastrointestinal and blood–brain barrier membranes, and the ability to release the drug in the presence of FBS progressively. In the 2D GBM cell model, using U87 and U251 cell lines, both compounds similarly reduced tumor cell viability. In 3D-bioprinted cell models, in the presence of an FBS-free medium, SI306-PD2 exhibited a more effective antitumor activity compared to SI306, reducing the proliferation and diameter of U251 spheroids grown within the bioprinted scaffold in a statistically significant manner. The analysis of proteins extracted from 3D scaffolds confirmed that SI306-PD2 inhibited Src activation more efficiently than SI306. Conclusions: Our study suggests that, when tissue permeability represents a discriminating characteristic, bioprinted cell models can provide a valid alternative for studying the cytotoxicity of new antitumor compounds. This approach has permitted us to ascertain the potential of the prodrug SI306-PD2 as a therapeutic agent for GBM, demonstrating better tissue penetration and antiproliferative efficacy compared to the precursor compound SI306.