Rotational atherectomy (RA) is an established technique for modifying heavily calcified and fibrotic coronary artery lesions. Despite its efficacy, the use of a high-speed rotating burr can provoke platelet activation and endothelial injury, thereby increasing thrombotic risk, promoting inflammation, and impairing vascular healing. This study investigated the effects of RA and its procedural characteristics on endothelial function and platelet activation by assessing circulating biomarkers. We prospectively analyzed 34 patients undergoing elective RA at a tertiary center. Blood samples were obtained before and 12–24 h after the procedure. Plasma levels of soluble E-selectin, soluble intercellular adhesion molecule-1 (ICAM-1), platelet factor 4 (PF4), P-selectin, and cluster of differentiation 40 ligand (CD40L) were measured. The study population had a mean age of 71 ± 8.9 years, and 73.8% were male. Cardiovascular comorbidities were prevalent, including diabetes (61.9%), hypertension (92.9%), hypercholesterolemia (42.9%), heart failure (45.2%), atrial fibrillation (21.4%), prior PCI (81%), and prior CABG (11.9%). RA significantly increased levels of P-selectin (55.5 ± 26.1 vs. 68.9 ± 26.5, p < 0.001), CD40L (2261.3 ± 2489.9 vs. 3602.0 ± 2428.5, p = 0.01), and PF4 (6054.7 ± 5751.8 vs. 10,877.6 ± 4979.7, p < 0.001). Moreover, mean burr speed correlated with CD40L elevation, while burr-to-artery ratio correlated with E-selectin increase (all p < 0.05). RA induces significant platelet activation and endothelial injury, with biomarker changes suggesting correlation with procedural parameters. These findings highlight the biological impact of RA and may inform strategies to optimize the safety of complex PCI.