Paediatric HIV spontaneous controllers (HSCs) are a unique and understudied population with potential to inform alternative treatment options for patients living with HIV. As HSCs are so rare and often not recognised prior to antiretroviral treatment (ART) initiation, it can be difficult for clinicians to optimally manage this group. We describe the diagnosis, history and management of three paediatric HSCs, two girls and a boy who were followed for 2, 1.25 and 10.4 years, respectively, before starting ART. All had low but detectable viral loads throughout follow-up but mostly marginally low CD4:CD8 ratios. The reason for starting ART in all was a gradual tendency to poorer virological control. This case series should assist in recognising paediatric HSCs. Clinical dilemmas arising in the management of paediatric HSCs include arriving at a correct HIV-positive diagnosis, correct diagnosis as an HSC, as well as whether to initiate ART. Decision-making for initiation of ART in paediatric HSCs should be individualised. Factors supporting ART initiation in these patients included increased frequency of viral load blips, increasing detectable viral load, CD4 percentage and CD4:CD8 ratio. Other factors included Hepatitis C serology and highly sensitive C-reactive protein. All three patients ultimately required ART, which supports universal initiation of ART in paediatric HSCs, but further research is required.