The risk of malaria outbreak surfaced in Vanuatu after Tropical Cyclone (TC) Pam in March 2015. In June and July 2015 we conducted malariometric surveys on the islands of Tanna, Aneityum, and Erromango in Tafea Province, where malaria elimination had been targeted, to determine if malaria incidence had increased after TC Pam. No Plasmodium infection was detected by microscopy and PCR in 3009 survey participants. Only 6·3% (190/3007) of participants had fever. Spleen rates in children aged ⩽12 years from Aneityum and Tanna were low, at 3·6% (14/387) and 5·3% (27/510), respectively. Overall bed net use was high at 72·8% (2175/2986); however, a significantly higher (P < 0·001) proportion of participants from Aneityum (85·9%, 796/927) reported net use than those from Tanna (67·1%, 751/1119) and Erromango (66·8%, 628/940). A recent decrease in malaria incidence in Tafea Province through comprehensive intervention measures had reduced the indigenous parasite reservoir and limited the latter's potential to spur an outbreak after TC Pam. The path towards malaria elimination in Tafea Province was not adversely affected by TC Pam.