The two unnamed men were hanged in a prison in the provincial capital Zahedan.
They were accused of drug trafficking.
Iranian authorities routinely execute dissidents on bogus charges such as armed robbery and drug smuggling.
Sistan-va-Baluchistan Province is home to Baluchis, a predominantly Sunni Muslim ethnic minority.
Iran has witnessed escalating unrest since 2006 in areas populated by Baluchis, who complain of discriminatory and repressive policies by the theocratic regime.
Since 2006, Iranian authorities have stepped up executions in the restive province in what many Baluchis believe is a response to a spate of attacks by dissidents on government and security officials.
