The station's feedback programme received numerous complaints that the anthem is "too loud and jingoistic" and prevents listeners from drifting off to sleep.
Responding to the complaints, Radio 4's network manager Dennis Nolan said the network will continue to play the anthem.
He said the national anthem is a big cultural symbol which has all kinds of emotional meanings and can be read in many different ways. He added that while for some, it may sound jingoistic, others may find the anthem comforting and encouraging.
Some people have suggested a quieter version of the anthem to be aired, but Nolan said it needed to remain "stirring".