Tama, which was made a railway official eight years ago, was credited with putting the rail firm back on track financially after drawing in thousands of tourists.
The 16-year-old cat died of heart failure on 22 June.
Dozens of company officials and thousands of fans turned out for Tama's Shinto-style funeral on Sunday, where she was elevated to the status of a goddess.
The president of Wakayama Electric Railway, Mitsunobu Kojima, also gave her the special title of "honorary permanent stationmaster", AP reports.
He said Tama had contributed an estimated 1.1 billion yen ($8.9m; £5.7m) to the local economy.
"She was affectionate with people and hard-working," one local resident said.
Another cat, called Nitama, has since become an apprentice station master.
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