Across tropical Africa, febrile children are treated for malaria either with or without confirmation thus resulting in failure to diagnose and treat other co-morbidities like urinary tract infections (UTI) and upper respiratory tract infection (URTI) that may coexist with malaria. This crosssectional study examined coexisting malaria with UTI and further assessed the antimicrobial susceptibility pattern of the isolated organisms among children aged <5 years presenting with fever. Between December 2012 and May 2013, 284 children were recruited from the Saint Francis Xavier Hospital, in the Central Region of Ghana through purposive sampling. Thick and thin blood films were used for the diagnosis of malaria and urine samples were collected in sterile, wide-mouthed, leak proof containers for culture and sensitivity. Organisms isolated were identified and tested for their antimicrobial sensitivity patterns using the Kirby-Bauer disc diffusion method. Prevalence of malaria with coexisting UTI was 15.8% with majority (58.0%) of the participants being female. Age was significantly (p=0.025) associated with malaria and UTI co-infection with the highest prevalence of co-infection (35.6%) recorded amongst the 13-24 months age group; gender was not associated with co-infection (p>0.05). Malaria parasitaemia (1+ to 3+) was significantly (p=0.001) associated with bacteriuria. Staphylococcus aureus (30.3%), Escherichia coli (20.4%) and Proteus species (5.3%) were isolated and these isolates were highly susceptible to Gentamicin (GEN), Ciprofloxacin (CIP) and Nitrofurantoin (NIT) but were resistant to ampicillin (AMP). Staphylococcus aureus was the predominant cause of the UTI and the isolates were highly resistant to ampicillin but susceptible to gentamicin, ciprofloxacin and nitrofurantoin.