The troops were riding an armoured vehicle when the bomb went off in New Rafah, a town on the border with the Gaza Strip, said officials who spoke on condition of anonymity because they were not authorised to speak to the media.
The armed group ISIL (ISIS) claimed responsibility for the attack in a statement on an ISIL-affiliated website.
In a similar attack last month, ISIL fighters ambushed a checkpoint in the town of Sheikh Zuweid, killing at least five troops and wounding at least six others.
Egypt has been battling armed groups in northern Sinai for years. Violence and instability there intensified after the 2013 military coup that removed Mohamed Morsi, an elected but divisive president, amid nationwide protests against his brief rule.
The fighters have carried out numerous attacks, mainly targeting Egyptian security forces, minority Christians, and those who they accuse of collaborating with the military and police.
Also on Thursday, the spokesman of Egypt’s armed forces, Lieutenant-Colonel Gharib Abdel Hafez Gharib, issued a statement saying nine troops were killed and wounded in clashes in Sinai.
However, he did not provide the breakdown of the casualties. It also remained unclear which attack he was referring to.
Gharib added the armed forces killed 13 fighters and confiscated 15 automatic rifles and ammunition in northern and central Sinai. He did not specify when exactly these killings happened.
The fight against armed groups in Sinai has largely taken place hidden from the public eye, with journalists, non-residents and outside observers barred from the area. The conflict has also been kept at a distance from tourist resorts at the southern end of the peninsula.