The carrier reported Tuesday net profit of 171.7 billion yen ($1.7 billion) for the fiscal year ending March 2013, the first year after emerging from bankruptcy.
Sales for the year edged up nearly 3 percent to 1.24 trillion yen ($12 billion).
The battery problems in 787 jets resulted in the worldwide grounding of the planes and forced flight cancellations for JAL.
Aviation authorities have been checking their safety, and have approved the changes Boeing made to the lithium-ion batteries.
Regional tensions set off last year by a territorial dispute reduced air travel to China. The weakening yen also hurt profit because of higher fuel costs, JAL said.