Around 700 people from the area gathered to show their opposition to the march, while more than 200 left-wing activists chained themselves to the station platform, delaying the arrival of the neo-Nazis' train by more than an hour.
The bus drivers were less than cooperative, forcing many of the neo-Nazis to walk into town. Their rally was several hours late and accompanied by loud protests nearby.
Bad Nenndorf in Lower Saxony has been the focus of neo-Nazi marches every year since 2006, because it was where the British army set up an interrogation centre for Nazis after the war.
Jürgen Trittin, head of the Greens' parliamentary party, spoke at an anti-Nazi rally there on Saturday, and said the protests were trying to make victims out of the perpetrators, which he called a “grandiose falsification of history.”
Sebastian Edathy of the Social Democratic Party (SPD) said, "We are neither ready to hand over our streets and our squares, nor the hearts and minds of the coming generation, to these enemies of humanity."
He said far-right extremism was a reality in Germany but should never be accepted as normal.
At least 2,000 police officers were in the town, while a surveillance drone flew over the more than 450 neo-Nazis. Last year around 580 showed up while in 2010 the number was more than 1,000.
The neo-Nazis had planned to go to Hannover, around 35 kilometres away, after their march in Bad Nenndorf – but cancelled this themselves, a police spokeswoman said. They are now planning a torch-lit march through Hannover at a later date.
Several hundred left-wing demonstrators gathered in Hannover in anticipation of the planned neo-Nazi march, and some clashed with the police. Around 50 people were briefly held, but no arrests were reported.