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Samardzija's deal is for five years and worth up to $7.25 million, a source close to Samardzija told ESPN's Joe Schad.
Once the deal is approved by the commissioner's office, Samardzija will join the Boise Hawks, an advanced rookie club of the Northwest League.
Samardzija will be able to play at Notre Dame this fall. His plan is to play professional baseball and football after graduating Notre Dame and he is a possible first round draft choice in the next NFL draft.
The deal is backloaded and Samrdzija would have to continue to play baseball in order to approach the maximum value of the contract.
The Valparaiso, Ind., native caught a record 15 touchdown passes last fall. He then went 8-2 with a 4.33 ERA in 15 starts for the baseball team.
Joe Schad is ESPN's college football reporter. Information from The Associated Press was used in this report.