The Lot 2 follow-on is for nine kits, plus spares, training, support equipment and engineering support.
The contract is worth $65.8 million, Boeing said.
"Combining the three major B-1 modifications into one installation will not only save taxpayer dollars but also will allow us to get the bombers back to the field much faster and with more capability," said Rick Greenwell, Boeing B-1 program director.
The IBS integrates three major modifications: an updated front and aft cockpit, a new diagnostics system and a new Link 16 data link.
Boeing said the initial Lot 1 contract, awarded last year, was four IBS kits, with civilian employees from Tinker Air Force Base installing the upgrades and with Boeing personnel providing engineering support.
"Lot 2 kit orders will begin immediately and the entire fleet will be upgraded by the end of 2019," the company said.