Thames Valley Police said Jacob Leland, 35, was charged with 14 counts of sexual offences against a teenage boy more than decade ago.
Leland, of Lincoln's Inn Fields, Camden, was employed at the school at the time of the alleged offences.
He is accused of five counts of engaging in non-penetrative sexual activity with a boy under 16 and four counts of engaging in penetrative sexual activity with a boy under 16.
He is also charged with three counts of causing or inciting a boy under 16 to engage in sexual activity and two counts of sexual assault on a male.
Police said the charges were in connection with incidents which occurred more than a decade ago in the Eton area.
Leland denied the charges at Reading Magistrates' Court on Wednesday, and is next due to appear at Reading Crown Court on December 4.
An Eton College spokesperson told the Telegraph newspaper that the school "firmly beside those former pupils directly involved, who have acted with great courage and dignity throughout"
The spokesperson added: "The welfare and well-being of our pupils is Eton's top priority.
"When safeguarding concerns arise they are dealt with in accordance with our established processes and we always work closely with the relevant authorities where appropriate, as we have in this case.
"Given the ongoing criminal process, we cannot comment further at this stage."
Eton College, a boarding school for boys aged 13 to 18, is one of the country's most well-known private schools.