Background: After the decrease in clinical malaria incidence observed in Mozambique until 2009, a steady resurgence of cases per year has been reported nationally, reaching alarming levels in 2014. However, little is known about the clinical profile of the cases presented, or the possible epidemiological factors contributing to the resurgence of cases. Methods: An analysis of surveillance data collected between July 2003 and June 2013 in the high malaria-transmission area of Ilha Josina Machel (Southern Mozambique) through a paediatric outpatient morbidity surveillance system was conducted to calculate hospital-based clinical malaria rates, slide-positivity rates, and minimum community-based incidence rates (MCBIRs) and incidence rate ratios per malaria season in children younger than 15 years of age. Clinical malaria was defined as a fever ≥37.5 °C or a reported fever in the previous 24 h with a positive blood smear. Yearly mean age, geometric mean parasitaemia (GMP) and mean packed cell volume (PCV) were also described for all clinical malaria cases and compared between seasons using DID analysis or ANOVA tests. Results: During the study period, the percentage of outpatient visits presenting with confirmed clinical malaria decreased from 51 % in the 2003–2004 season to 23 % in 2008–2009, followed by an increase back to 51 % in 2012–2013. The yearly mean age of cases significantly increased from 2.9 (95 % CI 2.8–3.0) in 2003–2004 to 5.7 (95 % CI 5.6–5.7) in 2012–2013, compared to non-malaria cases. An increase in mean PCV levels was also observed (p < 0.001), as well as in GMPs: from 5778 parasites/µL in 2002–2003 to 17,316 parasites/µL in 2012–2013 (p < 0.001) mainly driven by an increase in GMP in children older than 1 year of age. MCBIRs in infants decreased by 70 % (RR = 0.3, p < 0.001) between 2003–2004 and 2012–2013. Incidence diminished by a third among children 1- to 4-years between 2003 and 2007, although such drop was unsustained as observed in 2012–2013 (RR = 1.0, 95 % CI 0.9–1.0). Finally, the incidence among children 5–14 years was 3.8 (95 % CI 3.4–4.3) times higher in 2012–2013 compared to 2003–2004. Conclusion: Since 2003, Ilha Josina Machel observed a significant reduction of clinical malaria cases which was followed by an upsurge, following the national trend. A shift in the age distribution towards older children was observed, indicating that the changes in the transmission intensity patterns resulted in a slower acquisition of the naturally acquired immunity to malaria in children.