In a series of meetings over two days, the foreign secretary took flak from Iranian officials for not doing more to build on the nuclear deal signed with world powers in 2015.
"Relations between the two countries have not matched the potential expected in the post-JCPOA (nuclear deal) atmosphere," Rouhani told Johnson, according to a statement from his office.
There was similar criticism from the powerful parliament speaker, Ali Larijani, who met with Johnson yesterday and said other European countries had put in "much more effort".
A key focus of Johnson's visit had been efforts to secure the release of imprisoned British-Iranian Nazanin Zaghari- Ratcliffe.
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Zaghari-Ratcliffe, 39, is already serving a five-year sentence for her part in mass protests in 2009 -- which she denies -- and was due to face fresh charges in court today of "spreading propaganda".
The trial was expected to take place behind closed doors and it was not clear when any verdict would be announced.
"The foreign secretary discussed the full range of regional and bilateral issues, including banking matters and our concerns about the consular cases of dual nationals," a British foreign office spokesperson said.
The Zaghari-Ratcliffe case has become a top priority for Johnson after he mistakenly said last month that she had been training journalists in Iran -- a "slip of the tongue" used by the Iranian authorities to help justify the new charges.
Iran has been frustrated that the nuclear deal, which lifted sanctions in exchange for curbs to its nuclear programme, has not produced the expected windfall in trade deals -- mainly due to continuing US sanctions.
The husband of the jailed British-Iranian, Richard Ratcliffe, has claimed she is a pawn in Iran's efforts to extract the historic debt.
Johnson left Iran later today for the United Arab Emirates.
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