Following sporadic reports of post-treatment control of HIV in children who initiated combination antiretroviral therapy (cART) early, we here prospectively studied 284 very early cART-treated children from KwaZulu-Natal, South Africa after vertical HIV transmission to assess control of viraemia. 84% of the children achieved aviraemia on cART but aviraemia persisting to >36m was observed in only 32%. We observed that male infants have lower baseline plasma viral loads (p=0.01). Unexpectedly, a subset (n=5) of males maintained aviraemia despite unscheduled complete discontinuation of cART lasting 3m-10m (n=4), or intermittent cART adherence during 17m loss to follow up (n=1). We further observed in vertically transmitted viruses a negative correlation between type I interferon (IFN-I) resistance and viral replication capacity (VRC) (p<0.0001), that was markedly stronger for males than females (r=-0.51 versus r=-0.07 for IFNα). While viruses transmitted to male fetuses were more IFN-I sensitive and of higher VRC than those transmitted to females in the full cohort (p<0.0001 and p=0.0003), the viruses transmitted to the five males maintaining cART-free aviraemia had significantly lower replication capacity (p<0.0001). These data suggest that viraemic control can occur in some infants with in utero acquired HIV infection after early cART initiation, and may be associated with innate immune sex differences.