In 1960, Qureshi found employment with the Pakistan Atomic Energy Commission (PAEC), and was posted to the Atomic Energy Center in Lahore where his interest built in radiochemistry. Upon returning to Pakistan from Denmark in 1971, he joined the Institute of Nuclear Science and Technology (the national lab) in Nilore, working at the Nuclear Chemistry Division (NCD).
As early as 1972, Qureshi joined the team of scientists that began working on the equation of state of the radioactive decay element plutonium, while he established the computerized radiation detection chemical analysis laboratories at the Pakistan Institute of Nuclear Science and Technology in 1973. In 1974, Qureshi and his team was instrumental at the national laboratory when he was the first to confirm the detection of radiation emissions coming from Rajasthan in India. Hence, by using neutron activation analysis, confirming Pokhran-I the first Indian nuclear test, which India later announced was indeed conducted at the Pokhran Test Range. Notably, he led the team that balanced the chemical equation required for the exothermic chemical reaction in fission devices. By 1977, he discovered the technique for balancing the nuclear Q-value and energy balance in a boosted fission weapon.
Eventually, Qureshi headed the Nuclear Chemistry Division (NCD) at the Institute of Nuclear Science and Technology which was responsible for the multi-stage chemical process that separated, concentrated and isolated plutonium from uranium. At NCD, he also played a supervisory role in developing the Analytical Chemistry Group comprising modern and state of the art analytical chemistry laboratories such as the Analytical Chemistry Laboratory, Atomic Absorption Spectroscopy lab, Emission Spectrography lab, Chromatography lab, Electrochemical Analysis lab and radioisotope production labs. The Analytical Chemistry Laboratory was later certified by the International Atomic Energy Agency (IAEA), and oversaw the successful commissioning of the PARR-III reactor that went phase critical  in 1973.
Qureshi engaged in research about copper-nickel alloys after introducing the lattice dynamical method to evaluate the Cu/Ni alloys. Key and fundamental research on understanding neutron flux was carried out by Qureshi, for which he managed to secure patents from the IAEA. After the conclusion of the Pakistan's clandestine atomic bomb projects, he was appointed chief technical officer at the Pakistan Atomic Energy Commission (PAEC) in 1991; though he was more eager to return to academia.
Throughout his time at PAEC, Qureshi earned several scientific honors, including the Gold Medal and a Fellowship of the Pakistan Academy of Sciences in 1994. He was a recipient of the Sitara-i-Imtiaz (Star of Excellence) from the Government of Pakistan in 1992. In 1997, from the Iranian Government, he received the Khwarizmi International Award for advancing and understanding the "Nuclear analytical techniques development and application in Pakistan".