The benchmark Nikkei 225 index gained 0.61 percent, or 127.77 points, to end at 21,159.08, while the broader Topix index was up 0.26 percent, or 4.44 points, at 1,704.00.
A recent string of brighter news on North Korea helped buoy the market, said Makoto Sengoku, market analyst at Tokai Tokyo Research Institute.
In the latest development in efforts to solve the North Korean nuclear crisis, officials in Seoul announced Thursday that North and South Korea will hold a summit on April 27.
The dollar was changing hands at 106.64 yen against 106.86 yen in New York but well above the mid-105 yen range seen in Tokyo earlier Wednesday. Investors tend to rush to the Japanese unit as a safe bet in times of crisis or turmoil.
A weaker yen is positive for Japanese exporters as it makes their products more competitive abroad and inflates profits when repatriated.
But Sengoku added gains on the overall market were trimmed by declines in the technology sector following another Wall Street sell-off fuelled by fears of a regulatory clampdown.
"Even with the lower yen, investors are not all-out bullish," he said.
In Tokyo, leading e-commerce firm Rakuten lost 2.57 percent to 872.8 yen.
Panasonic dropped 3.96 percent to 1,503.5 yen as heavy selling hit the key battery supplier to Tesla, which faces US federal investigation over a fatal crash last week involving one of its cars.
Takeda Pharmaceutical tumbled 7.44 percent to 5,120 yen after it said it was considering buying Ireland-based drugmaker Shire as part of its attempts to boost overseas acquisitions.
The news of a possible takeover boosted Shire in London by more than 14 percent, putting its market value at 32 billion pounds ($45 billion).
Toyota closed down 0.29 percent at 6,842 yen and Nissan fell 0.45 percent to 1,094.5 yen after the automakers announced global production drops for February.