Its Real-Time Gross Settlement (RTGS) system is crucial for handling settlements between banks, handling an average £570 billion of payments a day.
A glitch was said to have been caused by a "failure in a piece of hardware".
It led to the Bank issuing a brief statement saying: "The Bank has been experiencing some technical IT problems today.
"There is no impact on critical payment and settlement services. Alternative procedures are in place where necessary.
"The Bank is acting to resolve these problems as soon as possible."
A source said that "procedures in place for this sort of eventuality are now operating".
The Bank's website underlines the importance of the system, stating: "As the final record of sterling interbank transfers, the resilience of the RTGS system is paramount.
"As such, it operates on fault-tolerant computer hardware which is replicated on a second site, and with the business operation also conducted on a split-site basis."
It is also used for paper-based cheque and credit clearings and Link, the UK's cash machine network.
RTGS is the system which operates the Bank's reserve accounts, effectively sterling current accounts for commercial banks.
These are among the safest assets a bank can hold and the ultimate means of payments between banks.
The Bank of England website explains: "Whenever payments are made between the accounts of customers at different commercial banks, they are ultimately settled by transferring central bank money (reserves) between the reserves accounts of those banks."