Chickpea is an important legume crop, characterized by its high nutritional value and abundant physiologically active compounds. Pulsed electric field (PEF), as an emerging non-thermal physical processing technology, has demonstrated unique advantages in regulating seed germination and the accumulation of secondary metabolites. In this study, chickpeas were subjected to germination combined with PEF treatment to optimize germination conditions, and the physiological and metabolic changes, as well as flavonoid biosynthetic patterns in chickpea sprouts under conventional germination and PEF-assisted germination were systematically investigated. The results showed that under the optimal conditions (12 h soaking, PEF treatment at 30 kV applied voltage, 6 µs pulse width, and 500 Hz frequency for 27 min, followed by 72 h germination), the total flavonoid content in chickpea sprouts reached a peak of 3025.27 ± 21.11 µg/g DW. Optimized PEF conditions markedly activated the enzyme activities of the phenylpropanoid pathway and induced the upregulated expression of their corresponding genes. Meanwhile, the activities of antioxidant enzymes and the expression levels of related genes in PEF-treated chickpea sprouts were also markedly enhanced. PEF can promote flavonoid accumulation and improve antioxidant capacity in chickpea sprouts by activating the phenylpropanoid metabolic pathway and the antioxidant system. This study contributes to the development of nutritious foods based on chickpea.