"We have looked at this thing from every which way," Thomas told the insider newsletter. "It doesn't make sense to get in. We don't see a chance to win. I don't want to be a second candidate against an incumbent."
His decision means Mourdock will likely have a clear shot against Lugar in the May primary. The state filing deadline is Feb. 21.
Thomas also said he would not endorse Lugar or Mourdock.
In 2010, Thomas spent $600,000 out of his own pocket to challenge then-Rep. Mark Souder (R-Ind.). Thomas lost his primary bid to Souder by about 14 points in what was a crowded GOP field.
Terri Henderson, 6, center, whose mother is El Salvador, attends a rally with members of Congress at Union Station's Columbus Circle to announce the Restore Opportunity, Strengthen, and Improve the Economy (ROSIE) Act on July 29, 2014. The legislation provides incentives for government contractors to pay a living wage and other benefits that would help low-income workers.