The benchmark Nikkei 225 index was up 0.11 percent, or 23.34 points, to close at 20,479.42, while the broader Topix index was up 0.04 percent, or 0.66 points, at 1,490.35.
Investors welcomed stability in foreign exchange rates as the dollar, which fell below 105 yen earlier this week, edged up against the Japanese currency, brokers said.
The figure of "105 yen is a critical line for many Japanese firms", said Daiwa Securities chief technical analyst Eiji Kinouchi.
The dollar fetched 105.84 yen in Asian afternoon trade, against 105.77 yen in New York late Tuesday.
"Today's trading was thin and directionless," said Yoshihiro Okumura, general manager at Chibagin Asset Management.
Kinouchi said trading had been affected by the US-China trade dispute and "the market will continue to be subject to the issue for now".
US President Donald Trump's repeated assertions that Beijing wants to make a deal to end the two countries' year-long trade war had cheered markets on Monday. But the optimism was short-lived since Chinese officials did not confirm any new talks.
In Tokyo, real estate firms led gains, with Mitsui Fudosan rising 2.24 percent to 2,528 yen and Mitsubishi Estate trading up 2.57 percent at 2,048 yen.
Nintendo rose 0.24 percent to 40,350 yen as Sony edged up 0.18 percent to 5,893, but Toyota fell 0.43 percent to 6,889 yen.