The shoe was thrown at Additional Sessions Judge Lokesh Sharma by the man, a relative of the murder victim, a court official said.
The official, who narrated the incident on condition of anonymity, said the incident happened when the judge was hearing another case.
The judge was not hit by the shoe and was unhurt, he said.
Manoj Kumar, 34, was immediately arrested and an FIR was lodged against him at the Saket police station under sections 186 (obstructing public servant in discharge of public functions) and 353 (assault or criminal force to deter public servant from discharge of his duty) of the IPC.