She had worked for the Bank for several years without mentioning this.
The Bank's code of conduct, which she helped to draw up, states employees must declare such connections.
MPs on the Treasury Committee said she "fell short of the very high standards" required and the committee said it had "set aside" its approval of her appointment.
Despite her resignation, she will take part in this week's interest rate setting decision on the Monetary Policy Committee. It will be her first and last time.
'Honest mistake'
Minutes after the Treasury Committee released its comments the Bank announced Ms Hogg's resignation.
Bank governor Mark Carney said: "While I fully respect her decision, taken in accordance with her view of what was the best for this institution, I deeply regret that Charlotte Hogg has chosen to resign from the Bank of England."
In her resignation letter, Ms Hogg said she was very sorry for not declaring her brother's role.
"It was an honest mistake: I have made no secret of my brother's job - indeed it was I who informed the Treasury Select Committee of it, before my hearing.
"But I fully accept it was a mistake, made worse by the fact that my involvement in drafting the policy made it incumbent on me to get all my own declarations absolutely right.
"I also, in the course of a long hearing, unintentionally misled the committee as to whether I had filed my brother's job on the correct forms at the Bank.
"I would like to repeat my apologies for that, and to make clear that the responsibility for all those errors is mine alone."
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