While the population of Tokyo as a whole is growing quite slowly, some parts of the city are experiencing change at a dizzying pace. This phenomenon is most visible in the massive construction projects at Shibuya, Shinagawa, and Tokyo Station.
In contrast to Tokyo’s slow and steady population growth, the following numbers (for stations on Tokyo Metro) are really quite massive.
Station Name: 2012 Ridership -> 2015 Ridership % Growth
Ikebukuro: 483,952 -> 548,839 +13.4 %
Kita-Senju: 287,433 -> 289,001 +0.5 %
Otemachi: 277,336 -> 313,620 +13.1 %
Ginza: 245,548 -> 245,208 0.0 %
Shibuya: 226,644 -> 216,687 (-4.4) %
Shimbashi: 223,335 -> 241,041 +7.9 %
Shinjuku: 220,154 -> 231,340 +5.1 %
Ueno: 212,509 -> 207,240 (-2.5) %
Takada no Baba: 186,629 -> 196,613 +5.3 %
Iidabashi: 169,830 -> 186,299 +9.7 %
Tokyo Station: 169,152 -> 196,687 +16.3 %
Toyosu: 160,196 -> 200,533 +25.2 %
Yurakucho: 152,102 -> 167,929 +10.4 %
Omotesando: 150,569 -> 174,394 +15.8 %
Kudanshita: 146,202 -> 166,390 +13.8 %
Shinjuku San-Chome: 102,605 -> 149,796 +46.0 %
All numbers are for on+off, and do not include “transfers” (“他鉄道との直通連絡駅および共用している駅の乗降人員”).
janejacobsjapan 
What stations are losing the most riders? Are Tokyo citizens densifying their center faster than new population arrives into the suburbs?
Tokyo is somewhat curious in that it rarely has densities much over 150 even in central districts. New York, Paris, and Hong Kong routinely see 300+ in central areas. My beloved Mexico City is like Tokyo in sustaining an even density around 150 from the center far out into the suburbs instead of dropping steeply away from a concentrated center. Still I expect to see both cities centralize a bit more.
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Among major stations, only Ueno seems to be losing riders. Over 3 years from 2012 to 2105, Tokyo Metro’s ridership at Ueno fell 2.5%, and JR’s ridership at Ueno fell 1.1%.
Over the same Period, Tokyo Metro lost 4.4% at Shibuya, and JR Shibuya lost 9.7%. Tokyu Shibuya gained 4.2% on its Toyoko Line and 3.5% on its Denen-toshi Line. I coudn’t find 2012 data for Keio’s Inokashira Line. Any decline at Shibuya is probably temporary, seeing as there are multiple major development projects underway (https://www.shibuyastation.com/shibuya-station-area-redevelopment-plan/).
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“From 2000 to 2005, population growth was observed in selected areas
of Tokyo. Growing areas include waterfront areas (Minato, Chuo and Koto
Wards), residential areas within Tokyo 23 Wards (Nerima, Setagaya, etc.)
and suburban residential areas (Machida City and Aoba-Ku, Yokohama
City). Condominiums (“mansion” or apartment for sale, not for rent) are
built in larger scale in these areas: the share of condominiums with more
than 100 units/building increased from 14% in 1995 to 58% in 2005, and
the share of apartments with more than 200 units/buildings is as high as
38% in 2005. On the other hand, population decline was observed in the
outer suburbs. People are coming back to the selected areas of Tokyo
including central Tokyo. (Ministry of Land, Infrastructure and Transport,
Government of Japan 2007).”
~http://www.thecandlelightclub.com/Sakura%20in%20Old%20Tokyo/9784431992660-c1.pdf
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“Population polarization [i.i. articulation] is striking even among the three major metropolitan areas, with the tendency of people to return to city centers. The overall population of Osaka Prefecture dropped for the first time in 68 years, but the population surged in central Osaka City.”
~https://www.mizuho-ri.co.jp/publication/research/pdf/eo/MEA160530.pdf [based on 2015 data]
Chart 4 from this report is a must-see (shows rapid population growth in central Tokyo, 2010-2015).
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