Most Japan itineraries include both, but if you're weighing which to prioritize with limited time, Tokyo and Kyoto represent the two poles of the country — hyper-modern capital versus preserved former capital.
Tokyo is dense, fast-moving, and endlessly varied by neighborhood — Shibuya's scramble crossing, Akihabara's electronics and anime shops, Shinjuku's neon nightlife. Kyoto is slower and more uniform in feel, built around temples, traditional wooden neighborhoods like Gion District and the sloped lanes of Ninenzaka & Sannenzaka, and a much lower skyline.
Tokyo's draws are modern and eclectic: teamLab Borderless, Tokyo Skytree, and neighborhood-hopping between Harajuku & Omotesando and Asakusa's older Senso-ji Temple. Kyoto is almost entirely about temples and gardens — Kinkaku-ji (Golden Pavilion), Kiyomizu-dera Temple, Fushimi Inari Taisha's thousands of torii gates, and the Arashiyama Bamboo Grove — with far more of them per city block than anywhere else in Japan.
Tokyo has the wider range — from Michelin-starred sushi to the Tsukiji Outer Market's street food, it covers every price point and cuisine. Kyoto specializes in kaiseki (multi-course traditional dining) and tofu cuisine, generally more refined and formal, reflecting its history as an imperial capital.
Tokyo is enormous — even hitting a handful of neighborhoods takes real train time. Kyoto is a fraction of the size and far more walkable, with most major sights reachable by bus or a short taxi ride, making it the easier city to see thoroughly on a tight schedule.
Choose Tokyo for scale, variety, and modern Japan — food, shopping, nightlife, and neighborhood culture. Choose Kyoto for temples, traditional architecture, and a slower, more contemplative pace. They're a 2.5-hour bullet train apart, and most travelers with more than five days do both — Tokyo first for the shock of scale, Kyoto second to slow down.