In 1990, he joined The New York Times as a news assistant, and was promoted to reporter in 1992. He served as chief of the Albany bureau as a political reporter, City Hall correspondent and Newark correspondent. Since 2000, he had been a special projects reporter for the Times' Metro desk. In 2003, he won the Pulitzer Prize for investigative reporting. In 2002, he wrote a series "Broken Homes" on the abuse of mentally ill adults in state-regulated homes. He broke the story on New York State Medicaid fraud in 2005.
From 2007 to 2011, Levy was the Times 's Moscow bureau chief. He received his second Pulitzer Prize in 2011 in the category of International Reporting for his reporting on corruption in Russia in cooperation with Ellen Barry. The jury awarded their "dogged reporting that put a human face on the faltering justice system in Russia, remarkably influencing the discussion inside the country.". Shortly before, in March 2011, Levy was named deputy editor of The New York Times's Metro section.
Levy is married to Juliane Dressner. They live with their three children: Danya, Arden and Emmett in Park Slope, Brooklyn. In Park Slope his children attended P.S. 321. For a period Levy enrolled his children in the New Humanitarian School in Moscow during his foreign correspondent work.
- 2012 National Magazine Award for Digital Media in Video for "My Family's Experiment in Extreme Schooling"
- 2011 Pulitzer Prize for International Reporting 
- 2010 George Polk Award for Foreign Reporting 
- 2009 Robert F. Kennedy Journalism Award
- 2003 Pulitzer Prize for Investigative Reporting  for "Broken Homes"
- 1998 George Polk Award for Local Reporting 
- Levy, Clifford J. "My Family’s Experiment in Extreme Schooling." The New York Times. September 15, 2011. 1. Retrieved on May 21, 2012.