He graduated from George Mason University with a bachelor of science degree in economics in 1983 and received his PhD in economics from Harvard University in 1987 with his thesis titled Essays in the theory of welfare economics. At Harvard, he was mentored by game theorist Thomas Schelling, the 2005 recipient of the Nobel Memorial Prize in Economics. He is married to Natasha Cowen, a lawyer.

Cowen has written papers on political philosophy and ethics. He co-wrote a paper with philosopher Derek Parfit arguing against the social discount rate. In a 2006 paper, he argued that the epistemic problem fails to refute consequentialist forms of argument.

Cowen has been described as a “libertarian bargainer” who can influence practical policy making, yet he endorsed bank bailouts in his March 2, 2009 column in The New York Times. In a 2007 article entitled “The Paradox of Libertarianism”, Cowen argued that libertarians “should embrace a world with growing wealth, growing positive liberty, and yes, growing government. We don’t have to favor the growth in government per se, but we do need to recognize that sometimes it is a package deal”.

In 2012, David Brooks called Cowen “one of the most influential bloggers on the right”, writing that he is among those who “start from broadly libertarian premises but do not apply them in a doctrinaire way”.