A group of men attacked Junaid Khan and his three brothers last month in an apparent row over seats as they travelled by train from New Delhi to their home in neighbouring Haryana state, killing him and injuring one of his brothers.
One brother said the attackers accused them of carrying beef, a meat popular among many Indian Muslims but shunned by most of the country's Hindus, who revere cows as sacred.
Haryana's deputy inspector Mohinder Singh said police acted on a tip-off and arrested the chief suspect, who officers believe stabbed Khan to death, in Dhule district of western Maharashtra state late Saturday.
"We arrested the main accused person today, just a little while ago, in Maharashtra. That makes six arrests in total now," Singh said, withholding the suspect's name and further information.
The other suspects were arrested last week.
India has been reeling from a spate of vigilante murders in recent months, especially targeting Muslims for allegedly killing cows or consuming beef.
Khan's murder drew thousands to the streets across Indian cities last week, with demonstrators calling for an end to the wave of mob violence under the slogan "not in my name".
Last year prime minister Narendra Modi criticised the vigilantes and urged a crackdown against groups using religion as a cover for committing crimes.
Critics say vigilantes have been emboldened by the election in 2014 of his right-wing Bharatiya Janata Party.
The slaughter of cows and the possession or consumption of beef is banned in most Indian states, with some imposing life sentences for breaking the law.
