Quarter the onion and mince the garlic. Grate the fresh ginger. Rinse fresh herbs and bean sprouts. Thinly slice the jalapenos.
Place chicken thighs in the bottom of the crockpot. Add quartered onion, minced garlic, grated ginger, star anise, and cinnamon stick on top.
Pour in chicken broth, then add fish sauce, soy sauce, and brown sugar. Stir gently to combine.
Cover and cook on low for 6 to 8 hours or high for 3 to 4 hours until chicken is tender and broth is flavorful.
Remove chicken thighs carefully. Shred the chicken using two forks. Discard onion quarters, star anise, and cinnamon stick from the broth.
Cook rice noodles according to package instructions, usually soaking in hot water or boiling for a few minutes until tender. Drain and set aside.
Divide noodles into serving bowls. Top with shredded chicken, then ladle hot broth over the top.
Garnish with bean sprouts, fresh basil, cilantro leaves, lime wedges, and sliced jalapenos. Squeeze lime juice to taste and serve immediately.