The president was speaking at a provincial rally in support of Turkey's troops in Syria, which was broadcast live on state television.
The incident has already been criticized by the pro-Kurdish Peoples' Democratic Party (HDP) that opposes Ankara's operation in the Afrin region.
The embattled leader was addressing members of Turkey's ruling party Saturday in Kahramanmaras when he noticed Amine Tiras crying. "We should develop joint projects", the president said.
"Her Turkish flag is in her pocket ..."
Russian TV network RT called Erdogan's remarks "a freaky act of patriotism".
The president's latest comments however do not appear to have dampened the enthusiasm of his supporters of him or of his Syria offensive - they do not appear concerned that Erdogan's own sons have evaded military service while he routinely emphasises the importance of martydom as a means of securing Turkey's future.
Freedom Watch with Judge Napolitano: Judge Napolitano and former ambassador to the U.N., John Bolton, discuss President Erdogan of Turkey warning that Turkey would extend its military operation in Syria, which could potentially bring their forces into confrontation with the U.S.at the same time Turkish forces are fighting Kurds, whom the USA has armed.
Turkey has a longstanding culture of nationalist militarism, with popular slogans such as "Every Turk born a soldier".
Mr. Erdogan recently made an alliance with the right-wing Nationalist Movement Party to bolster his chances for coming elections and has used the military campaign to improve his stance with nationalists. "Oh my God, I am shocked".
He was also trashed on Twitter, with one user noting "you don't wish death for a child, you never say: 'God willing'".
The mainstream press, which has been increasingly under the thumb of the government, did not focus on the girl's tears. Her lips trembling, she stood ramrod-straight as she gave a military-style salute.