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Farrell, 25, is set to move past 500 international points this weekend against Fiji, and is second in the England all-time list behind Wilkinson.
Asked whether Farrell could one day beat his record of 1,179 points, Wilkinson said: "I have no doubt.
"I would be very surprised if Owen Farrell didn't go on to score way, way more," he told BBC Sport.
"500 points for a guy who is 25 years old, you don't have to do the maths but if he plays until he is 35, he will be in a good place."
Wilkinson has been involved in the England camp this year as a kicking and skills consultant, and says he can identify with the way Saracens fly-half Farrell approaches the game.
"Sometimes when we are discussing things, you hear something that you definitely correspond with," said Wilkinson, who on Thursday became one of 12 new inductees into the World Rugby Hall of Fame.
"[Working with England] is a really exciting opportunity," Wilkinson, who scored the winning drop goal in the 2003 World Cup final, continued.
"But there is no telling or teaching, it's kind of a sharing, and therefore there has to be room in all of us to keep growing. I am also there to learn."
Wilkinson has also compared the current midfield combination of Farrell, who has scored 497 points for England, and fly-half George Ford to his partnership with inside centres Will Greenwood or Mike Catt.
"Both those guys were phenomenally important to me in my career, in the way they supported me, got the best out of me, and helped me to uncover more about myself," Wilkinson explained.
"With Owen and George, they are both very, very open individuals, both very humble - but not because they have been taught what to say, but genuinely it's who they are.
"There is not a script being followed here. They are following enthusiasm, passion and serious devotion.
"It's very similar when you mention names like Mike Catt and Will Greenwood, it all makes perfect sense. It's just about having good people in there."
You can hear more from Jonny Wilkinson on the Matt Dawson Rugby Show on BBC Radio 5 live from 19:30 GMT on Thursday, 17 November.

Hawkins held off the challenge of the defending champion, Moses Kipsiro of Uganda, clocking a time of of 60 minutes 22 seconds.
Kenya's Joel Kimutai came home in third ahead of England's Chris Thompson.
Another Kenyan, Betsy Saina, claimed victory in the women's race with a course record time of 67:20.
Hawkins is the first Scot to win the great Scottish Run since 1983, and it rounds off a memorable year which saw him finish ninth in the marathon at the Rio Olympics in the summer.
After setting the pace alongside Kipsiro and Kimutai in the early stages, Hawkins broke away on his own and always looked in control as he left the three-time Commonwealth champion Kipsiro trailing in his wake.

Officer Phil O'Neill did not consider the fact he could not see Daniel Adewole an emergency situation and returned 18 minutes later.
The 16-year-old, who had epilepsy, was later found unresponsive in his cell at Cookham Wood in Rochester.
Asked if he thought he should have gone back sooner, Mr O'Neill said: "I do."
Another officer, Sharon Bignell, told the inquest she had not unlocked Daniel's cell because the teenager "could have been hiding" and could have attacked her.
The inquest, being carried out by coroner Patricia Harding, continues.

The men aged 38, 42, 45 and 46, were arrested after a car was stopped in the Ringfort Road area, in Hazelbank, on Thursday night.
They were questioned at Antrim police station.
Police said their enquiries were continuing.
World Cup winner Jonny Wilkinson has backed Owen Farrell to overtake his England points record.
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Scotland's Callum Hawkins claimed victory in the Great Scottish Run in Glasgow, setting a new Scottish half-marathon record in the process.
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A prison officer went for a cigarette when he could not find a teenager who was supposed to be in his cell, an inquest heard.
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Four men arrested in Londonderry by police investigating dissident republican activity are released unconditionally.