The governor of Kilis province said another two soldiers were injured when a border post was attacked from Syria.
Turkey responded with heavy weapons, reportedly killing one IS militant.
It is the latest violence to hit Kurdish-dominated south-east Turkey, three days after 32 people were killed by a bomber linked to IS in Suruc.
Also on Thursday, a Turkish traffic policeman was shot dead in the city of Diyarbakir. The officer and a colleague were attacked while attending a collision.
The second officer was badly injured. No group has yet said that it was behind the shooting of the officers.
“Unfortunately, one of our non-commissioned officers has been martyred and two sergeants injured,” Kilis Governor Suleyman Tapsiz told Turkey’s Anadolu news agency.
He added that the two wounded soldiers were in a stable condition.
In response, Turkish tanks opened fire on IS-controlled targets inside Syria, Turkish media report.
The two attacks on Thursday have added to the bloodshed in the area of Turkey nearest to IS-held territory.
On Monday, a suicide blast killed 32 people in the mainly Kurdish town of Suruc, near the Syrian border.
On Wednesday, two other policemen were shot dead in their home in Celanpinar, 160km (100 miles) from Suruc.
The military wing of the outlawed Kurdistan Workers’ Party (PKK) said it was behind that attack.
They said it was revenge for the killings in Suruc, and said the men had collaborated with IS fighters.
On Thursday morning, Turkish security forces arrested three people for killing the two men in Celanpinar, Anadolu said.
A 20-year-old Turkish student has been identified as the suicide bomber who killed the 32 youth activists in Suruc.
The attacker, named by local media as Seyh Abdurrahman Alagoz, was an ethnic Kurd from Turkey’s south-eastern province of Adiyaman and reportedly had links to IS militants.
Alagoz’s mother told the newspaper Radikal (in Turkish) that her son was a former student at Adiyaman university who had gone “abroad” six months ago with his brother.
“I don’t know what they were doing abroad, they never said. They were just telling me they were fine,” Semure Alagoz said.
A senior Turkish official told Reuters that he believed the bomber, who he did not name, had travelled to Syria last year with the help of a group linked to IS militants.
Monday’s suicide bombing claimed 32 lives and injured 100 others, making it one of the deadliest attacks in Turkey in recent years.
The activists were mainly university students, who were holding a news conference when an explosion ripped through the group at the Amara Cultural Centre.
They had been planning to travel to Syria to help rebuild the town of Kobane. The youngest victim was Okan Pirinc, who was 18, according to the Turkish media.
Many in Turkey feel the government has not done enough to support the Kurds in their fight to combat the threat of IS fighters across the border in Syria – something denied by Ankara.
On Thursday, one IS fighter alleged to have crossed from Syria into Turkey was shot dead by the youth wing of the PKK in Istanbul.
The group said the man had travelled from Kobane to Istanbul for treatment seven months ago, and had been planning attacks in the city.