The announcement came after a high-level ministerial meeting in Nairobi on cooperation including on security, as well as trade and the movement of people.
The frontier had been officially closed in 2011 because of attacks on Kenyan soil by Somalia’s Al-Shabaab Islamist militant group.
“We have resolved that the border between Kenya and Somalia will be reopened in a phased manner within the next 90 days, effective today,” Interior Minister Kithure Kindiki said, adding that a first crossing should be opened in 30 days.
The two nations had announced plans in July last year to reopen the frontier at talks between then Kenyan president Uhuru Kenyatta and his Somali counterpart Hassan Sheikh Mohamud but it never materialised.
Kindiki said they would work together on security, improving information sharing and mechanisms for cross-border collaboration.
“Kenya and Somalia are continuously experiencing both inter and intra-security challenges emanating from Al-Shabaab,” he added.
Kenya is a major contributor of troops to the African Union military operation against the Al-Qaeda-linked Al-Shabaab, which has been waging a violent insurgency in Somalia for more than 15 years.
Relations between the two nations have been dogged by a maritime border row as well as Somali accusations of Kenyan meddling in its affairs, while Nairobi has accused Mogadishu of using it as a scapegoat for its own political and security problems.
By Fred Odanga Azelwa.