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The order comes amid a debate in the country about the rise of aggressive nationalism in India under the Hindu-right wing Bharatiya Janata Party government.
A wheelchair-bound activist was assaulted in the western state of Goa last month for not standing up to the national anthem, sparking widespread criticism.
The court said everyone in the hall should rise for the anthem and the national flag should be displayed on the screen, said lawyer Abhinav Srivastava, who filed a petition on the alleged misuse of the anthem on behalf of a non-governmental organization.
“Time has come that people must feel and show respect to the national anthem, the symbol of constitutional patriotism,” broadcaster NDTV quoted the judges as saying in the order.
While the anthem is on, all theatre exits will be closed.