The spa gene of Staphylococcus aureus encodes protein A, a key virulence factor contributing to molecular typing. spa typing provides valuable information encoding diversity and transmission, particularly for methicillin-resistant S. aureus (MRSA), which remains a major public health concern. A one-year prospective surveillance study was conducted involving S. aureus bacteremia (SAB) patients admitted to Haji Adam Malik General Hospital, Medan, Indonesia. SAB isolates were phenotypically analysed for cefoxitin resistance using the VITEK-2 system and genotypically characterised by PCR for the mecA and spa genes. Spa typing of the X region was performed at Apical Scientific Laboratory (Selangor, Malaysia), and clustering was analysed using the Based Upon Repeat Pattern (BURP) algorithm. A minimum spanning tree (MST) was constructed with Ridom SeqSphere to assess genetic relatedness. Clinical outcomes were compared between MRSA and MSSA clusters. A total of 120 SAB patients were included, equally divided into MRSA and MSSA groups. The dominant spa types included t852 (12.5%), t5422 (9.2%), and t4171 (7.5%). In-hospital mortality was 28.3%, significantly higher in MRSA compared with MSSA (p-value 0.015, OR 2.76). ICU admission occurred in 20.9% of cases. MRSA isolates predominantly clustered in a single group (Cluster 1), consistent with clonal transmission, whereas MSSA isolates displayed greater genetic heterogeneity across multiple clusters. This prospective surveillance highlights the clonal expansion of MRSA within a tertiary care setting and supports the utility of spa typing as a practical molecular tool for monitoring transmission and guiding infection control strategies.