Farina Arshad worked as Second Secretary at Pakistan High Commission in Dhaka, Foreign Office said in statement.
It said that she was constantly being "harassed" by the Bangladeshi authorities.
"The Government of Pakistan twice summoned the High Commissioner of Bangladesh and a strong protest was lodged against the treatment meted out to her," it said.
The Foreign Ofiice said that an incessant and orchestrated media campaign was launched against her on spurious charges linking her with so-called terrorists.
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The development came as media reports quoting Bangladeshi investigators said a detained operative of outlawed Jamaatul Mujahideen Bangladesh (JMB) told them that the outfit maintained links with Arshad, who provided them money.
According to the reports, the detained JMB operative has told police that he travelled with the diplomat in her car in the city when she gave him Taka 30,000 (USD 382) while he made 48 trips to Pakistan in the past two years.
Last week, the premier Dhaka University also scrapped ties with all Pakistani varsities amid continued outrage.
In January, a Pakistani High Commission staffer in Bangladesh was asked to leave the country after being found indulging in terror financing including circulating Fake Indian Currency Notes.