The missiles hit Pakistan-managed Kashmir and the locations in the country's eastern Punjab province.
The government said India launched missiles at multiple locations in Pakistan and in Kashmir, Pakistan.
The strike comes after last month's deadly attack on Indian-managed Kashmir tourists, tensions among nuclear-weapon neighbors, with New Delhi blaming Islamabad, denying any involvement.
Several explosions were heard earlier on Wednesday in the Pakistan-managed Kashmir capital Muzaffarabad city.
The missiles hit the site in Kashmir, which is managed by Pakistan and the eastern part of the country's eastern Punjab province, according to three Pakistani security officials mentioned by the Associated Press News.
The Indian government said in a statement that Indian troops attacked "Pakistan's terrorist infrastructure, Pakistan-occupied Jamu and Kashmir attacked places where terrorist attacks were attacked on India," the Indian government said in a statement.
"Our actions have been centrally focused, measured and non-localized in nature. There are no military facilities targeting Pakistan. India has shown considerable limitations in selecting goals and methods of implementation," it said.
Pakistani troops said at least 12 people were killed and 12 others were injured in the Indian attack.
A Pakistani military spokesperson told broadcaster Geo that there are at least five locations, including two mosques. He said Pakistan's response was in progress and no details were provided.
Al Jazeera's Kamal Hyder reported that the cities of Muzaffarabad and Kotli were targets of India's strike.
Tensions among nuclear-weapon neighbors have intensified after the attacks on Indian tourists from Indian-Admir Pahalgam last month.
India accused Pakistan of violence, with 26 people killed and vowed to respond. Pakistan denies that it has something to do with the murder.
"Just gets it," Indian troops said in an article on X earlier Wednesday after India's strike.
Nitasha Kaul, director of the Center for Democratic Studies, said the strike was “very worrying.”
"The affected persons who are affected again will be the people of the region, Kashmiris were arrested between the competition and the postures of all and competitors and the attitudes of India and Pakistan," Kaul told Al Jazeera.
She said that, though, the escalation is not surprising because within India…because of a particularly overnationalist government, domestic pressure has increased for more militarist responses.
"In this sense, sadly, it's the countdown to the countdown, and hopefully it won't go beyond what these strikes have already happened," Kaul added.