Herrera, who was visiting pupils at Astley Sports College along with striker Radamel Falcao, acknowledged that his answer might not be popular amongst Manchester United supporters - but couldn't bring himself not to choose the four-time Ballon d'Or winner.
The Spanish midfielder was taking questions from pupils and was quoted by Manchester Evening News reporter Samuel Luckhurst, who attended the event.
Herrera picks Messi over Ronaldo
Asked who is ideal signing would be, Herrera responded: "This is not good for United fans but I would say Lionel Messi."
Falcao was also asked the same question. The Colombia international decided to pick Paul Scholes, the Manchester United legend who brought an end to his glittering playing career at the end of the 2012-13 campaign.
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Messi linked to United this season
Messi was linked with a shock move to Manchester United earlier this season, when the Argentina international was reportedly at odds with Barcelona's current head coach Luis Enrique.
United are one a handful of clubs in world football who could potentially find the astronomical funds to sign the 27-year-old, who is considered by some to be not only the best player of his generation, but the greatest player of all time.
With 391 goals in 459 appearances, Messi has broken just about every Barcelona goalscoring record since making his debut for the Catalan giants in October 2004. He is also the top scorer in the history of La Liga.
Messi set to stay at Barcelona
However, despite the intense speculation surrounding his future and the fact Herrera would love to play alongside the South American genius, it seems Messi is destined to stay at the Camp Nou.
It's understood that Messi and Enrique have sorted out their differences - or put them to one side, at least - while the Barcelona No. 10 is scoring goals for fun again. Crucially, it looks like he is enjoying his football once more.
Messi has scored 37 goals in 34 appearances so far this season - and hasn't scored fewer than 38 goals in a full campaign since 2008-09. In the 2011-12 season he scored a quite ridiculous 73 goals in all competitions for Barcelona.
Ronaldo's stats are similar, but the Portugal captain is now on the wrong side of 30 and appears to be slowing down a little following a spectacular start to the season.
Herrera right to choose Messi over Ronaldo
He will always occupy a special place in the hearts of Manchester United supporters following his six years at Old Trafford, but Herrera is right to select Messi over the current holder of the Ballon d'Or trophy.
It's unlikely that fans will ever see Messi in a Manchester United shirt - but it's certainly nice to dream.
Manchester United fans: would you choose Messi or Ronaldo for Louis van Gaal's squad? Tell us by leaving a comment in the box below!