"Secretary of Homeland Security Kirstjen Nielsen will be leaving her position, and I would like to thank her for her service." Trump tweeted.
Trump added that Customs and Border Protection Commissioner Kevin McAleenan would become the acting chief of the US Department of Homeland Security (DHS).
Earlier, local media reported, citing sources in the Trump administration, that US Homeland Security Secretary Kirstjen Nielsen was expected to offer her resignation on Sunday evening during a meeting with Trump.
CBS News reported that it was not clear whether Kirstjen intended to resign voluntarily or was pressured to step down.
Kirstjen was confirmed as Homeland Security Secretary December 2017. Prior to that appointment she had been chief of staff to John Kelly during his term as the DHS secretary.
Nielsen later said in a statement that during her term in office she managed to enhance security of the country.
Nielsen did not provide reasons for resignation, saying that it was her own decision.
The outgoing homeland security secretary noted that the department "prevented the disruption of US elections and guarded against foreign interference in democracy."