There were no immediate reports of new casualties or serious damage, but the U.S. Geological Survey said the quake was felt in El Salvador and neighboring Costa Rica.
The new tremor, centered 34 miles (56 kilometers) south of the capital city of Managua, surprised people at restaurants and supermarkets, where the shelves swayed strongly, throwing many products to the ground.
It also disrupted the water service in many towns around the capital, where people continued to feel aftershocks as the government deployed soldiers and police officers to oversee emergency response.
Firefighters paid visits to villages south of Managua and reported seeing cracking in the walls of houses and other buildings.
"There are a lot of homes that will have to be demolished completely," said Rosario Murillo, government spokeswoman and Nicaragua's first lady.
Earlier, the government raised the number of people injured in the Thursday evening quake from 23 to 200. It also said that a 23-year-old woman had died of an apparent heart attack after the quake. No deaths had been reported as a result of Friday's shake.
Although the magnitude of Friday's earthquake was higher, it struck much deeper, making it less likely to cause damage.
In the capital city of Managua, 300 homes were damaged and at least 20 were destroyed by Thursday's quake, said one of the mayor's deputies, Fidel Moreno.
Authorities ordered the demolition of two old buildings that had withstood the earthquake of 1972 that killed 10,000 people. Hospitals began discharging patients with minor illnesses so they could have beds available in the event of injuries from an aftershock or new quake.
President Daniel Ortega said that he raised the country's alert level to red, meaning government officials were evacuating everyone at risk of harm from aftershocks or new quake.
The alert also meant schools and businesses closed in the capital and in the northwestern city of Leon. There was much less traffic in the streets.
Despite the warnings, hundreds had gathered at the Metropolitan Cathedral of Managua for a religious act in preparation for Holy Week when the stronger earthquake hit.
"We were feeling better even though there were some aftershocks but this last quake was very strong. We are worried again," said Miguel Ugarte.
On Thursday night, officials took 155 people out of neighborhoods northeast of the capital city due to risk of landslides. One of the shelters was still housing 22 families on Friday.
The government said roughly 800 homes were damaged in the town of Nagarote and surrounding areas, about 30 miles (50 kilometers) northwest of the capital.
Friday's quake struck at 3:29 p.m. local time (20:29 GMT), and was centered about 6 miles (11 kilometers) east-southeast of the town of Nandaime. It had a depth of 85 miles (138 kilometers).
The USGS said Thursday's quake struck at 5:27 p.m. local time (23:27 GMT), and was centered about 11 miles (18 kilometers) southeast of the city of Larreynaga. It had a depth of 6.2 miles (10 kilometers).