Police later confirmed a man had been detained under the Mental Health Act and said the station would be reopened as soon as possible.
They had earlier said the station was closed after "reports of a man on the tracks claiming to have a bomb".
Charing Cross station this morning, more police on blues and twos on way as I walked down The Strand... pic.twitter.com/NmuDUqnXdg— Michael O'Sullivan (@ProSecurityMag) June 22, 2018
A British Transport Police spokesman said: "Officers were called to Charing Cross underground station at 6.35am today after receiving reports of a man on the tracks claiming to have a bomb. Officers from the Metropolitan Police and BTP specialist firearms officers also attended.
"Both the underground and mainline stations were evacuated as a precautionary measure and a cordon was put in place whilst officers dealt with the incident."
The spokesman added: "A 38-year old man was detained by officers and has been held under Section 136 of the Mental Health Act and taken to a place of safety."
Witnesses reported seeing armed police swarm on the station as passengers were cleared from the surrounding area.
Tube and rail services were both affected by the incident after police were called.
Loads of police including armed response at Charing Cross. Underground shut off and asking people to move away. pic.twitter.com/nZlIxqJZ8m— alan buckingham (@ogs88) June 22, 2018
Charing Cross this morning.— Dave Ellis (@fullback03) June 22, 2018
Police and fire 🔥services everywhere. pic.twitter.com/OlbjufAVQI
Alan Buckingham tweeted: "Loads of police including armed response at Charing Cross. Underground shut off and asking people to move away."