The New York-based group said an Afghan identified as Gholamreza H. was hanged on October 30. He was 19 when the execution was carried out but had been convicted for a murder committed on November 20, 2006, when he was 17.
Human rights groups have criticized Iran for sentencing minors to death. Iran says it only carries out the death penalty when a prisoner reaches the age of 18.
"It is tragic that Iran is continuing to kill juvenile offenders," Clarisa Bencomo, Middle East children's rights researcher at Human Rights Watch, said in a statement. "Iran urgently needs to end its isolated position and abolish these executions."
In Tehran, an Iranian judiciary official said he was not aware of the case when asked about it at a news conference.
Rights groups had praised Iran when it seemed to have ended the practice in October. But a judiciary official later clarified Iran's position, saying juvenile offenders could still face execution for murder but not for other capital crimes.
Iran regularly rejects accusations of human rights abuses, saying it is following Islamic sharia and accusing Western governments of double standards.
Since January 2005, Iran has been responsible for 26 of 32 known executions of juveniles worldwide, Human Rights Watch said.