CERN Director-General Rolf Heuer and the Chairman of the Pakistan Atomic Energy Commission Ansar Parvez signed the agreement here in presence of Prime Minister Nawaz Sharif.
The membership will help Pakistan in establishing a sustained and institutionalised relationship with CERN, local media reported.
The potential benefits include training of scientists, engineers and students, getting commercial contracts from CERN for local industry, acquiring of old and used equipment from CERN and provision of high profile international projects.
"Today's event is also a testimony to the fact that whenever provided an opportunity, the people of Pakistan are capable of standing up to any international standard," he said.
"Pakistan has been a strong participant in CERN's endeavours in science and technology since the 1990s," said Heuer. "Bringing nations together in a peaceful quest for knowledge and education is one of the most important missions of CERN," Heuer said.