Naek was brought up in Karachi, Sindh, Pakistan. After graduating from high school, he was accepted at the Sindh Muslim Law College, where he earned an LLB in law. Later, he went on to attend the post-graduate school of the University of Karachi where he earned an MA in Economics. His political career began in 1971, when he served as Assistant Director at the Directorate of Labour and Social Welfare of the provincial Government of Sindh. He then was a Civil Judge and First Class Magistrate from 1971 to 1975. He was elected General Secretary of Karachi Bar Association during mid-1985-90. He also served as Deputy Attorney General of Pakistan from 1994 to 1996 in the second Benazir Bhutto government.
Naek enrolled as Advocate of local court in 1970, advocate of high court in 1976, and of Supreme Court in 1990. He resigned from the judicial service after serving as civil judge for two years and became an active member of the PPP in the mid-1970s.[4]
Naek was arrested in 1995, after leading a demonstration against the dictatorial rule of General Zia Ul Haq. He was held in Central Prison, Karachi, for about six months along with 10 other lawyers.[5]
Although Naek was associated with the PPP for three decades, he only shot to prominence when he fought the corruption and criminal cases against Benazir Bhutto and Asif Ali Zardari during Pervez Musharraf's rule in and out of Pakistan. It was during these extremely difficult years of Zardari that Naek earned his trust. Before and after becoming the President of Pakistan, Zardari always consulted him on legal matters and other issues.[4]
Naek contested the 2016 Supreme Court Bar Association elections for President, against Rasheed A. Razvi.[6] Naek however lost the election with a large margin.[7]