Today is my one thousandth lesson with you. Time goes by so quickly.
We've had one thousand lessons together. I can't believe how fast time flies.
ーToday is my one thousandth lesson with you. Time goes by so quickly.
「今日はあなたとの1000回目のレッスンです。あっという間だ」
one thousandth lesson with you で「あなたとの1000回目のレッスン」
Time goes by so quickly. で「時の経つのが早い・あっという間だ」
ーWe've had one thousand lessons together. I can't believe how fast time flies.
「私たちは一緒に1000回レッスンをしました。時が経つのが早くて信じられない」
to have one thousand lessons で「1000回レッスンを受ける」
time flies で「時間が経つのは早い」
ご参考まで！
"Today marks my 1,000th lesson with you. Time really flies."
"Today marks my 1,000th lesson with you. Time really flies."
"This is my 1,000th lesson with you today. It went by so fast."
"I can't believe this is my 1,000th lesson with you already."
「今日でちょうど1000回目」
英語では
Today marks my 1,000th lesson.
がとても自然です。mark は「節目を迎える」という意味です。
ちょうどを強調したいなら exactly を入れられます。
・Today marks exactly my 1,000th lesson with you.
カナダ 
アメリカ合衆国 
