Foreign Office said in a statement that the decision was conveyed to Indian High Commissioner Gautam Bambawale who was summoned to foreign ministry.
"The Foreign Secretary (Aizaz Chaudhry) summoned the Indian High Commissioner today and conveyed the decision of the Government of Pakistan to declare Surjeet Singh, an official of the Indian High Commission, as persona non-grata," the statement said.
The Foreign Secretary expressed deep concern over the activities of the Indian official that were in violation of the Vienna Convention and the established diplomatic norms, it said.
The Indian High Commission has been asked to make urgent necessary arrangements for Singh and his family to leave Pakistan by October 29.
Earlier on Thursday, India declared Pakistan High Commission staffer Mehmood Akhtar in New Delhi as persona non-grata for espionage activities after he was caught by Delhi Police with sensitive defence documents, including deployment details of BSF along the Indo-Pak border.
"Akhtar has been declared Persona Non-Grata and he along with his family has to leave India by this Saturday. He stated that he had joined Baloch regiment of the Pakistani Army in 1997. He came on deputation to the ISI in 2013. In fact, it was Mehmood Akhtar, who resorted to subterfuge by concealing his real identity. Mehmood Akhtar was posted in September 2013 to the Pakistan High Commission, where he is currently working," MEA official spokesperson Vikas Swarup told the media.
Responding to the allegation by Pakistan Foreign office about manhandling of Akhtar, Swarup said the staffer was treated with diplomatic courtesy even though he did have a diplomatic passport.
He asserted that India has not violated any provision of the Vienna Convention.
"The denial that has come out from Pakistan (on Mehmood Akhtar) would say that this is something which has by now become quiet characteristic. If today Pakistan is feeling isolated, it's because of its misguided policies. The people of Pakistan should urge the government to adopt policies that favour peace," he added.
Pak high commission official asked to leave India in 48 hours for spying
Nawaz Sharif warns India over 'ceasefire violations'
Busted Pakistani spy ring may have roots in BSF
How do you solve a problem like Pakistan?
India's terrorism narrative needs a rethink