The boat called Da Jin Man 88 was carrying five crew members when it was seized by China's coast guard in waters near Taiwan's Kinmen islands on July 2 for violating Beijing's seasonal fishing ban.
The Kinmen islands are administered by Taipei but are located just a few kilometres (miles) from China's mainland.
Four of the crew were released in August while the boat and its captain were freed on Friday.
Taiwan's coast guard escorted the boat to Penghu, an archipelago where it is registered, and arrived at around midnight (1600 GMT), a Taiwan coast guard official told AFP on Saturday.
In a statement late Friday, Taiwan's coast guard said the boat left the Chinese city of Quanzhou at around 2:00 pm on Friday after "penalty procedures were completed".
The official did not provide details about the fine, but Taiwan media reported that two politicians in Penghu had helped arrange payment of more than 210,000 Chinese yuan (US$29,000).
China's Taiwan Affairs Office confirmed in a statement Friday that "punitive measures" had been taken against the captain and that he had been freed.
China claims self-ruled democratic Taiwan as part of its territory and has not renounced the use of force to bring the island under control.
Beijing maintains a near-daily presence of naval vessels and warplanes around the island to pressure Taipei into accepting its claims of sovereignty.
Chinese coast guard ships have also been spotted around Taiwan's outlying islands, at times briefly entering its restricted waters.
A series of incidents involving boats from both sides have fuelled tensions across the narrow waterway separating Taiwan and China.
In February, the capsizing of a Chinese fishing boat while being pursued by Taiwan's coast guard further strained relations after two members of the Chinese crew died.
Taiwan insisted its coast guard was following legitimate procedures after the Chinese vessel entered "prohibited waters", but Beijing accused them of "seeking to evade their responsibilities and hide the truth".
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