At least 19 people were killed at the Monday Market in the Borno State capital, Maiduguri, at about 12:40 pm (1140 GMT) when it was packed with shoppers and traders.
Hours later, a suspicious vehicle that had been stopped at a checkpoint outside the city of Potiskum, in neighbouring Yobe, exploded at a police station as its driver was being taken in for questioning.
A police officer accompanying the car and the driver were killed, an officer said. Potiskum has been a repeated target for militant violence.
Both blasts came a week after a major Boko Haram attack on the fishing town of Baga in northern Borno State, which is believed to be the worst in the bloody six-year insurgency.
The town and at least 16 nearby settlements in and around Lake Chad were burnt to the ground and at least 20,000 people forced to flee their homes.
"For five kilometres (three miles), I kept stepping on dead bodies until I reached Malam Karanti village, which was also deserted and burnt," one survivor, fisherman Yanaye Grema, said.
But there was no independent corroboration of the huge numbers of dead cited locally.
The US State Department said Boko Haram's recent escalation of attacks on civilians "shows no regard for human life" and called for those responsible to be brought to justice.
"The United States abhors such violence, which continues to take a terrible toll on the people of Nigeria and the broader region, including Cameroon," it added.
- Remotely detonated? -
Boko Haram were seen as behind the attack in Maiduguri as it has increasingly used women and young girls as human bombs in their deadly campaign for a hardline Islamic state.
Civilian vigilante Ashiru Mustapha said the blast happened as the girl was being searched at the entrance to the market.
"The girl was about 10 years old and I doubt if she actually knew what was strapped to her body," he told AFP.
Witness Abubakar Bakura said: "The blast split the suicide bomber into two and flung one part across the road.
"Among the dead are two vigilantes who were searching the girl. I am pretty sure the bomb was remotely controlled."
A Red Cross official, who declined to be named, warned: "Many people sustained life-threatening injuries."
Borno State police spokesman Gideon Jubrin told reporters 19 people were killed and 18 others were injured but warned that the death toll could rise.
The market in the Borno state capital was cordoned off as health officials began the grim task of sifting through the wreckage and collecting body parts.
An attack at the same market on December 1 killed more than 10 people, and a week earlier more than 45 people lost their lives in an attack there.
On July 1, at least 15 people were killed in another suicide attack there blamed on the militants.
- Female recruits -
Boko Haram launched its first female suicide attack in June last year in the northern state of Gombe and there have been a spate of bombings since, including four in a week in the city of Kano in July.
The same month a 10-year-old girl was found in Katsina state wearing a suicide vest, prompting fears that young girls were being forced into becoming human bombs rather than through ideological motivation.
Forced conscription of young men and boys by Boko Haram has been well-documented. Last July, three women said to be "female recruiters" for Boko Haram were arrested.
An alleged trainer of women bombers was also detained in Kano in August with up to 16 "trainees".
Boko Haram, fighting for the creation of an Islamist state, is now said to be in control of all three borders of Borno state with Niger, Chad and Cameroon, as well as dozens of towns and villages in Borno and the neighbouring states of Yobe and Adamawa.
Security analysts said the Baga attack was likely against civilian vigilantes assisting the military and was an ominous sign of increasing violence before general elections next month.
On Friday, militants fought running battles with troops in the Yobe state capital, Damaturu, leading to the destruction of a mosque, shops and a market.
The attack was said to be a reprisal for an offensive by civilian vigilantes and local hunters against a Boko Haram enclave in southern Yobe on Tuesday.