Combine first 5 ingredients in a medium saucepan; bring to a boil. Partially cover, reduce heat, and simmer 30 minutes. Drain. Discard onion and thyme. Place peas on a jelly-roll pan; let cool 30 minutes.
Heat a small skillet over medium heat. Add fennel seeds; cook 3 minutes or until toasted, stirring occasionally. Combine fennel seeds, oil, vinegar, mustard, and pepper in a medium bowl, stirring with a whisk. Add peas; toss to coat. Stir in chives.