In the final chapters of Irene Hunt's young reader's novel Across Five Aprils, we are not actually directly told what happens to John Creighton after the war. However, we can deduce what happens based on what we are directly told.
Based on Chapter 11, we know that John has survived the war because the last letter that comes to Nancy tells of the Union troops successfully driving the Confederates out of Nashville. John also writes about some news of Bill, whom no one has heard from since Pittsburgh Landing. John finds Bill among the Confederates taken prisoner at Nashville and is granted permission by his captain to talk with Bill "like brothers ought to talk." Hence, even as late as Chapter 11, we know that both Bill and John are still alive.
In Chapter 12, the book's final chapter, Jethro is devastated by the news of Lincoln's assassination. Also, while Jethro is out laying in the grass at Walnut Hill in April, feeling furious that Lincoln was killed and devastated by the fact Jethro cannot leave the farm to pay his respects to Lincoln in Washington, he hears footsteps and sees that his brother-in-law Shadrach has returned. Shad informs him that Jenny has come back too, though Shad plans to leave for college and take Jenny with him. Nevertheless, Shad promises to stay and help with the farm until John comes home. Hence, due to Shad's promise, we can surmise that John successfully returns home from the war and continues his life on his farm with his wife Nancy. Be that as it may, many obstacles stood in the way of a soldier's safe return home from the Civil War even once the war was over; therefore, we can't truly be certain of what happens to John after the war and can only surmise.