Lerner received a BA in physics from Columbia University and did graduate work in physics at the University of Maryland, College Park, before pursuing a career in popular science writing.

In 1984, he began studying plasma phenomena and laboratory fusion devices, performing experimental work on the dense plasma focus. Lerner received funding from NASA's Jet Propulsion Laboratory in 1994 and 2001 to explore whether the dense plasma focus could be an effective ion thruster to propel spacecraft. He believes that it can also be used to produce useful aneutronic fusion energy, in a process he calls "Focus Fusion".

Lerner is a critic of the Big Bang model and advocates an infinitely old Universe. In 2006 he accepted an invitation to be a Visiting Scientist at the European Southern Observatory in Chile, offered at the initiative of fellow Big Bang critic and MOND enthusiast Riccardo Scarpa.

Lerner is also an active general science writer, estimating that he has had about 600 articles published. He has received journalism awards between 1984 and 1993 from the Aviation Space Writers Association.

The Big Bang Never Happened: A Startling Refutation of the Dominant Theory of the Origin of the Universe (1991) is Lerner's controversial book rejecting mainstream Big Bang cosmology and advancing instead a non-standard plasma cosmology originally proposed by Hannes Alfvén in the 1960s. The book appeared at a time when results from the Cosmic Background Explorer satellite were of some concern to astrophysicists who expected to see Cosmic microwave background anisotropies but instead measured a perfect blackbody spectrum with no variation across the sky. Lerner referred to this as evidence that the Big Bang was a failed paradigm. He also denigrated the observational evidence for dark matter and recounted a well known cosmological feature that superclusters are larger than the largest structures that could have formed through gravitational collapse in the age of the universe.

As an alternative to the Big Bang, Lerner adopted Alfvén's model of plasma cosmology that relied on plasma physics to explain most, if not all, cosmological observations by appealing to electromagnetic forces. Adopting an eternal universe, Lerner's explanation of observed cosmological evolution relied on a proposed a model of thermodynamics attributed in part to the work of Ilya Prigogine under which the universe has no definite age but continually increases in order...in defiance of the second law of thermodynamics. Lerner also criticized modern cosmology as being equivalent to the epicycle after epicycle complexities of Ptolemaic astronomy.

Lerner's criticisms of the Big Bang theory have been contradicted by physicists and cosmologists who have reviewed his book. The size of superclusters is a feature that has been limited by subsequent observations to the end of greatness and explained in the astronomical journals as arising from a power spectrum of density fluctuations growing from the quantum fluctuations predicted in inflationary models. Anisotropies were discovered in subsequent analysis of the both COBE and BOOMERanG experiments and were more fully characterized by the Wilkinson Microwave Anisotropy Probe.

While there was favorable reaction from non-experts to Lerner's book, physical cosmologists who have commented on the book have generally criticized it. In particular, Edward L. Wright, who teaches cosmology and astrophysics at UCLA, has criticized the specifics of Lerner's alternative cosmology asserting that his alternative model for Hubble's Law is dynamically unstable, that the number density of distant radio sources falsifies Lerner's explanation for the cosmic microwave background, and that Lerner's explanation that the helium abundance is due to stellar nucleosynthesis fails because of the small observed abundance of heavier elements. Wright has also directly criticized Lerner for making errors of fact and interpretation. Lerner has directly disputed Wright's critique.

While at Columbia, Lerner participated in the 1965 Selma March and helped organize the 1968 Columbia Student Strike.

In the 1970s, Lerner became involved in the National Caucus of Labor Committees, an offshoot of the Columbia University Students for a Democratic Society. Lerner left the National Caucus in 1978, later stating in a lawsuit that he had resisted pressure from the US Labor Party, an organization led by Lyndon LaRouche, to violate election law by channeling profits of an engineering firm to the organization.

More recently, Lerner sought civil rights protection for immigrants as a member and spokesman for the New Jersey Civil Rights Defense Committee.