Diagnostic tools for the management of acute osteomyelitis (OM) and septic arthritis (SA) have improved over the last decade. To investigate the influence and availability of magnetic resonance imaging (MRI) and nucleic acid testing (NAT), a retrospective cohort study was done. Patients admitted with acute OM or SA between 2005 and 2014 were identified using ICD-10 discharge codes. Ninety-six children were identified: OM, n = 45; SA, n = 42; and OM + SA, n = 9. Diagnostic imaging was performed in 100% of OM or OM + SA and 95% of SA patients. MRI was performed in 85% of OM patients, 26% of SA patients and 100% OM + SA patients. In patients with OM or SA, concomitant joint/bone involvement was detected in 24 and 36% of patients, respectively. In 58% of patients, a pathogen was detected (Staphylococcus aureus, Streptococcus pyogenes and Streptococcus pneumoniae being most common). Blood and tissue culture were positive in 41 and 86% for OM patients and in 14 and 41%, respectively, for SA patients. In 42% of patients, no pathogen was identified, of which 40% had no material for blood or tissue culture/NAT taken.