The poll, by consumer magazine Which?, found 56 per cent of ScotRail customers are content with the company – the seventh-place score of the 19 firms surveyed across the UK.
More than 7,000 regular travellers took part in the survey, with Merseyrail found to have the highest customer satisfaction score at 70 per cent.
Virgin Trains, which operates the West Coast mainline, and East Coast, the publicly owned operator of the East Coast mainline franchise, scored 64 per cent and 59 per cent respectively.
ScotRail was rated third-best regional operator after Merseyrail and Chiltern Railways.
Which? executive director Richard Lloyd said: “It’s disappointing to see some train companies consistently falling down on the basics of customer service, with dirty and overcrowded carriages and toilets that don’t work.
“Seven rail franchises end in the next two years and we want to see passengers’ experiences put right at the heart of the tender process so companies respond to consumer expectations and can be held to account if they don’t.”
According to the survey, carried out in November, 16 per cent of passengers across the UK experienced a delay on their last journey, with this figure rising to 26 per cent for commuters.
Just over a fifth of all commuters said they were likely to have stood on their last journey, while 11 per cent of passengers said toilets were not in good working order.
A ScotRail spokesman said: “We came third in the ranking for regional train operators and seventh out of 19 for the UK as a whole.
“We always welcome feedback from customers and will be studying the results in more detail for further ways we can improve. Our performance levels have held up well in recent weeks and we are looking to build on that.”
The overall satisfaction scores were based on satisfaction with a company and the likelihood of customers recommending the company. On average, those surveyed had travelled by train 32 times in the previous 12 months.
Which? also asked what passengers felt would improve their journeys and what they would be prepared to pay more for.
Lower ticket prices were top of the wanted list (60 per cent), with 80 per cent saying fares were too high.
People also wanted to see more carriages at peak times (35 per cent), promotions on ticket prices (29 per cent), wi-fi as standard (20 per cent) and improved punctuality and reliability (18 per cent – rising to 29 per cent for commuters only.)
A spokesman for the rail industry body the Rail Delivery Group said: “As we acknowledged last month, when the independent watchdog’s far more comprehensive survey found that more than four out of five passengers were satisfied with their overall journey, the industry needs to build on the improvements it has delivered over the last 15 years.
“We are always keen to get feedback from customers, whether good or bad, which has helped the industry attract record numbers of passengers and cut complaints by three quarters in a decade.”
But Bob Crow, leader of the RMT transport union, said: “Once again this survey shows that Britain’s privatised railways are delivering lousy service to the public, while money that could be invested in capacity and upgrading is siphoned off into multi-million pound profits for the rich.”
Published last month, the independent National Passenger Survey produced by watchdog Passenger Focus found satisfaction with ScotRail had fallen by three per cent to 87 per cent.