The 2016 Nippon Professional Baseball (NPB) Draft was held on October 20, 2016, for the 52nd time at the Grand Prince Hotel Takanawa to assign amateur baseball players to the NPB.

It was arranged with the special cooperation of Taisho Pharmaceutical Co. with official naming rights.

Only the first round picks were allowed to be contested with all picks from the second round onward being based on table placing in the 2016 NPB season in a waiver system.

From the third round the order was reversed continuing in the same fashion until all picks were exhausted.

[1] Due to Tokyo Yakult Swallows manager Mitsuru Manaka's mistake at the 2015 edition of the draft, losing tickets in the lottery were made blank as to avoid confusion with winning tickets emblazoned with "Negotiation Rights Acquired.