[4] He is the gold medalist at the 2010 Youth Olympics and he won the World Junior Table Tennis Championships in 2010 (doubles) and 2011 (singles).

At the 2009 World Junior Table Tennis Championships, Niwa reached the quarterfinals in the men's singles event before he was defeated by Lin Gaoyuan.

Niwa qualified for the 2009 World Table Tennis Championships in Yokohama, Japan by defeating Josef Simoncik in the qualification tournament.

At the 2011 Manama World Junior Table Tennis Championships, he won the gold medal in the men's singles event, defeating Lin Gaoyuan of China.

[7] Partnering with Kenta Matsudaira, Niwa overcame the Chinese pair of Wang Hao and Zhou Yu to win the 2012 World Tour Polish Open doubles title.

He partnered Kenta Matsudaira in the doubles event and reached the third round before losing to compatriots, Jun Mizutani and Seiya Kishikawa.

At the 2013 World Tour Japan Open in Yokohama, the "Niwa-Matsudaira" tandem lost in the finals against compatriots, Jin Ueda and Maharu Yoshimura.

Niwa won the 2014 World Tour Russian Open title in the men's singles event, defeating England's Paul Drinkhall in the final.

The Niwa/Yoshimura pair reached the semi-finals where they lost to Chinese pairing and eventual champions Fan Zhendong and Xu Xin in the men's singles event, he reached the quarter-finals, defeating Dimitrij Ovtcharov in the fourth round, and losing to Fan Zhendong in the quarterfinals.

[13] Niwa retired from international competition in November 2022 stating that he wanted to "pass the baton on to the next generation and support them" but will continue to actively compete within Japan.

At the 2017 World Table Tennis Championships Men's Doubles event, the pair won a joint bronze medal.

The following month, at the 2017 World Tour Japan Open, Niwa/Yoshimura reached the finals before losing to Ma Long/Xu Xin in three straight games.

Koki Niwa and Jun Mizutani were expected to play doubles in the team event (alongside Tomokazu Harimoto as the ace player) at the Tokyo Olympics in 2021.

Mizutani noted the uniqueness of having a doubles pair with two left-handed players and stated that their objective was to make the match as un-normal as possible.

At the 2011 Pro Tour Germany Open U21 Men's singles final, Niwa won in full games over Kim.