Magnetic Resonance Imaging (MRI) is a powerful, non-invasive tool widely used in preclinical research to investigate anatomical, functional, and molecular processes in small animal models. Ensuring both high-quality imaging and animal welfare requires adherence to best practices grounded in the 3Rs principles: Replacement, Reduction, and Refinement. Therefore, a schematic outline, a step-by-step workflow, from pre-imaging preparation to post-imaging recovery, is necessary to standardize procedures and promote reproducibility. Key considerations include the careful selection and administration of anesthetic agents. Proper anesthesia management is essential, as it directly affects both animal well-being and the integrity of imaging data by minimizing physiological artifacts. Among others, isoflurane is favored in MRI imaging for its rapid pharmacokinetics, minimal physiological impact, and fine-tuned controllability. Detailed protocols cover experimental setup, including positioning in MRI-compatible cradles, and the use of supportive equipment to maintain physiological stability, such as heating systems, respiratory monitoring, ECG, and temperature regulation. Post-imaging care is equally important, with guidance on recovery monitoring, supportive interventions to ensure ethical treatment. Establishing Standard Operating Procedures (SOPs) for each stage of the entire imaging process, ensures safe and effective small animal handling in MRI studies. This chapter is intended for researchers, veterinary staff, and imaging technicians committed to maintaining ethical standards while achieving scientific rigor in experimental MRI settings.