The play-off semi-final defeat to Sunderland means the Blues will spent a third successive year confined in the third tier of English football.
A return to the Championship was tantalising, but failed to come to fruition.
Nevertheless, there was still significant progress made in Kenny Jackett’s second season at the helm.
After finishing 2017-18 with 66 points, Pompey finished this term four places and 22 points better off.
They’ll again be looking to build on it next term and there’s plenty of positives that should be taken into account.
Here are 10 of them…
1. Checkatrade Trophy success
Of course, promotion was the main aim for Pompey this season.
But to have a new piece of silverware in the Fratton Park trophy cabinet does soften the blow slightly.
The Fratton faithful were given a day to remember at Wembley.
Fans of the younger generations got to watch their team at the national stadium, revelling in a memorable afternoon in the capital.
The final itself couldn’t have been much better. Goals, high-octane action, late drama and a penalty shootout triumph for Jackett’s troops which yielded the trophy.
2. Blessing in disguise
The Blues will spend an eighth successive season outside the Championship.
But there's the argument Pompey wouldn't have been ready for the second tier if they'd have gone up.
Even when Jackett's men topped League One, they weren't exactly blitzing their way past teams. In fact, many have agreed a fourth-place finish was actually an over-achievement.
The Championship is a completely different ballpark compared to League One, though.
In fact, the leap is arguably the biggest between two divisions in the football pyramid.
Of the clubs who will definitely be in the second tier next season, nine have been in the Premier League in the past five years.
Wage packets well into the tens of thousands of pounds are the norm, likewise transfer fees worth millions.
It's likely Pompey would have had one of the smallest budgets in the tier. This season, Rotherham held that status and were relegated.
So another year of strengthening ahead of a Championship return could be a blessing in disguise.
3. Bolton’s points penalty
Nobody likes to see a team in financial problems – especially Pompey fans given they’ve been through the same tribulations.
But next season relegated Bolton will start with a 12-point deduction after entering administration.
It means that a side that drops down from the Championship will have a significant disadvantage.
So often the clubs that are relegated League One pushing for an immediate return to the second tier.
Look at Barnsley and potentially Sunderland this term. Look at Wigan, Blackburn and Rotherham 12 months earlier.
But competing for a top-two spot will certainly be tall order for Bolton.
4. Other teams entering the division
Assessing the other teams that are entering League One, you wouldn’t expect too many of them to be pushing for automatic promotion.
Ipswich and Rotherham both join Bolton from the Championship.
Tractor Boys boss Paul Lambert has spoken about rebuilding the club around young players. That suggests they might be happy with a season of stability rather than a promotion push.
Rotherham, meanwhile, will likely be up there challenging – as they did last season when they went up via the play-offs.
In terms of the sides entering from League Two, a repeat of Luton’s achievement of back-to-back promotions seems unlikely.
The Cowley brothers have done a magnificent job at Lincoln but they face the challenge of managing in the third tier for the first time.
Bury are experiencing financial troubles the, while manager Ryan Lowe could depart to Plymouth.
MK Dons went up on the final day and Newport and Tranmere are fighting for the final berth in the play-off final.
5. Clarke money can be reinvested
With Pompey confined to the third tier for another season, it looks almost certain Matt Clarke will leave this summer.
The Blues’ prized asset has far too much quality to spend another year in League One.
If Jackett’s men had been promoted, there was the possibility of retaining Clarke and getting his first full season in the Championship under his belt.
But that now looks improbable.
The centre-back will want to test himself in the second tier – a level he more than capable operating at given his performances against Norwich and QPR in the FA Cup.
But fans can at least take solace from the fact Pompey will get a substantial fee for the 22-year-old.
That cash could be reinvested to bring in several quality players instead.
6. Away form
Pompey ended the campaign as League One’s elite road warriors.
Jackett’s men amassed 45 points on their travels, placing them at the summit of the away table by six points.
In all competitions, the Blues delivered 20 victories, which was only bettered by Premier League champions Manchester City (21) among clubs in the leading six tiers of the English game.
Ultimately, it was Pompey’s Fratton Park record which let them down, dropping 26 points on their own patch.
However, if they remedy that next campaign and keep up their sterling away form then surely promotion will be yielded.
7. Close’s hurtling progress
After Ben Thompson was recalled to Millwall in January, there was a significant void to fill in the middle of the park.
However, Ben Close took up the mantle impeccably.
A bit-part player before Christmas, the Southsea ace was magnificent in the second half of the campaign.
Close scored eight goals in 24 appearances – not bad for a holding midfielder – and improved in all areas of the game.
The academy graduate is only going to get better and a fine campaign could be ahead for him.
8. Curtis will return fresh
In the first half of the season, Ronan Curtis was earning rave reviews.
Goals, assists, passionate performances and a senior Republic of Ireland breakthrough – he could barely put a foot wrong.
However, Curtis was out of sorts in the final few months of the season.
By his own admission, he lacked the confidence he had before Christmas, while his freak finger injury couldn’t have helped.
Many believe the winger's dip in from was because his hectic schedule eventually caught up with him.
Curtis been on the go since January 2018, with the League of Ireland starting the following month.
He only had a two-and-a-half week break before reporting for pre-season duty at Fratton Park following his move from Derry City.
And when international breaks have gave some of his team-mates a weekend off, he's been away with his country.
His campaign is not yet over as he meets up with Eire on May 26, with the hope he'll be involved in their European Championship qualifiers against Denmark and Gibraltar next month.
However, he’ll be handed an additional 10 days to recharge his batteries and should then come back raring to go.
9. Full pre-season schedules for Cannon and Morris
There weren't too many opportunities for Pompey’s permanent January arrivals.
Andy Cannon and Bryn Morris, signed from Rochdale and Shrewsbury respectively, both had spells on the treatment table after moving to Fratton Park.
The former made just two appearances, while Morris featured eight times in total.
When they both returned from their injuries, chances proved limited.
Both are held in high regard by Jackett, though, and he feels they are capable of stamping their authority on his side.
When they have featured, they’ve displayed glimpses of their capabilities.
Cannon and Morris will both have a full pre-season under their belts and should benefit from that.
10. Harnessing their hurt
The holidays will be booked and the players will have their deserved holiday this summer.
But that’s not to say they’ll still not be hurting. In fact, it'll be the opposite.
While sitting by the pool, they’ll be wondering what they could have done differently – as individuals and as players.
Those feeling will remain until the campaign gets under way in August.
And all that frustration needs to be harnessed in pursuit of promotion.
When the Blues suffered play-off heartbreak at Plymouth three years go, just look how they bounced back the following year.