Cowan, who arrived back with the rest of the team in Dunedin yesterday morning after a lengthy journey from Perth, said it was somewhat of an empty feeling arriving back in the country.
"We've done a lot of work this year off the field and had a good leadership group, with a good bunch of senior players," he said.
"But we haven't got the rewards on the field."
Cowan said the team had been in good spirits, but admitted it had not been a great way to end the season, with three straight losses on tour.
The side lost to the Sharks, Lions and Force on tour to finish 11th on the table, the same result as last year.
"When you reflect on it, it's not nice to lose three games in a row.
"We weren't far away and we have been close all year.
"But that doesn't cut it in this competition," Cowan said.
The aim now for coach Glenn Moore and the Highlanders management was to keep the core of the side together.
"You look at the Chiefs and the Hurricanes.
"They've had the same sides for the last two to three years and they are now reaping the rewards."
The Highlanders had a long flight to Dunedin, leaving their Perth hotel about 5pm (local time) on Sunday and then flying through the night, arriving in Auckland at 5.45am yesterday, before a quick change and flight to Dunedin.
After leaving the sunny skies of Perth and the temperature in the mid 20s, it was a shock for most of the players, dressed in shorts and T-shirts, to arrive in a windy and raining Dunedin, with the temperature outside at the airport barely above 5degC.
There would be player interviews and debriefings during the week, as the season winds down for the southern franchise.
Players are set to return to their home provinces some time next week.
Cowan said he had enjoyed the captaincy in his first year, although a few more wins would have helped.
Cowan's season with the Highlanders may be over but he is likely to still have a run at Carisbrook as he should be in the All Blacks side which takes on the French in the first test of the season on June 13.
